Starting phenix.real_space_refine on Sun May 11 21:39:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i7w_35235/05_2025/8i7w_35235.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i7w_35235/05_2025/8i7w_35235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i7w_35235/05_2025/8i7w_35235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i7w_35235/05_2025/8i7w_35235.map" model { file = "/net/cci-nas-00/data/ceres_data/8i7w_35235/05_2025/8i7w_35235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i7w_35235/05_2025/8i7w_35235.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.040 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: 5 Type Number sf(0) Gaussians S 60 5.16 5 Cl 1 4.86 5 C 5396 2.51 5 N 1451 2.21 5 O 1553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8461 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2328 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 280} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1274 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'TRANS': 158} Chain breaks: 3 Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'OKL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.17, per 1000 atoms: 0.61 Number of scatterers: 8461 At special positions: 0 Unit cell: (110.805, 85.905, 131.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 60 16.00 O 1553 8.00 N 1451 7.00 C 5396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 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=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.0 seconds 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 14 sheets defined 34.6% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 29 through 54 removed outlier: 4.068A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 89 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 97 through 130 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 140 through 166 removed outlier: 5.124A pdb=" N HIS A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.817A pdb=" N ALA A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 223 through 260 removed outlier: 3.718A pdb=" N LYS A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 266 through 294 removed outlier: 3.597A pdb=" N ARG A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'B' and resid 6 through 32 removed outlier: 4.251A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 removed outlier: 3.598A pdb=" N ILE B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 removed outlier: 4.249A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 216 " --> pdb=" O HIS B 213 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY B 217 " --> pdb=" O CYS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.660A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 351 removed outlier: 4.236A pdb=" N ASN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 removed outlier: 3.946A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'D' and resid 7 through 22 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.059A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.659A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA3, first strand: chain 'B' and resid 185 through 190 removed outlier: 10.256A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.599A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS C 337 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 63 removed outlier: 3.564A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 103 removed outlier: 6.575A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 150 through 151 removed outlier: 3.743A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 198 through 202 removed outlier: 3.894A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 209 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.098A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.716A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 295 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.631A pdb=" N LEU E 20 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.416A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.933A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE E 216 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE E 212 " --> pdb=" O CYS E 159 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.799A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1074 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: 2.37 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2734 1.34 - 1.47: 2168 1.47 - 1.59: 3654 1.59 - 1.71: 0 1.71 - 1.83: 88 Bond restraints: 8644 Sorted by residual: bond pdb=" C07 OKL A 401 " pdb=" O08 OKL A 401 " ideal model delta sigma weight residual 1.214 1.398 -0.184 2.00e-02 2.50e+03 8.51e+01 bond pdb=" C10 OKL A 401 " pdb=" O11 OKL A 401 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.24e+01 bond pdb=" C15 OKL A 401 " pdb="CL17 OKL A 401 " ideal model delta sigma weight residual 1.692 1.784 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C10 OKL A 401 " pdb=" N09 OKL A 401 " ideal model delta sigma weight residual 1.390 1.324 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C07 OKL A 401 " pdb=" N09 OKL A 401 " ideal model delta sigma weight residual 1.384 1.328 0.056 2.00e-02 2.50e+03 7.83e+00 ... (remaining 8639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 11490 1.90 - 3.79: 169 3.79 - 5.69: 35 5.69 - 7.59: 7 7.59 - 9.49: 4 Bond angle restraints: 11705 Sorted by residual: angle pdb=" N VAL A 27 " pdb=" CA VAL A 27 " pdb=" C VAL A 27 " ideal model delta sigma weight residual 111.91 108.66 3.25 8.90e-01 1.26e+00 1.34e+01 angle pdb=" N PRO A 31 " pdb=" CA PRO A 31 " pdb=" C PRO A 31 " ideal model delta sigma weight residual 110.70 114.65 -3.95 1.22e+00 6.72e-01 1.05e+01 angle pdb=" CA PRO A 31 " pdb=" C PRO A 31 " pdb=" N PRO A 32 " ideal model delta sigma weight residual 117.93 121.75 -3.82 1.20e+00 6.94e-01 1.01e+01 angle pdb=" C07 OKL A 401 " pdb=" N09 OKL A 401 " pdb=" C10 OKL A 401 " ideal model delta sigma weight residual 129.77 120.34 9.43 3.00e+00 1.11e-01 9.87e+00 angle pdb=" C12 OKL A 401 " pdb=" C10 OKL A 401 " pdb=" N09 OKL A 401 " ideal model delta sigma weight residual 109.84 119.22 -9.38 3.00e+00 1.11e-01 9.78e+00 ... (remaining 11700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.18: 4682 27.18 - 54.37: 383 54.37 - 81.55: 27 81.55 - 108.74: 5 108.74 - 135.92: 1 Dihedral angle restraints: 5098 sinusoidal: 1981 harmonic: 3117 Sorted by residual: dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 146.24 -53.24 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" C03 OKL A 401 " pdb=" C04 OKL A 401 " pdb=" C05 OKL A 401 " pdb=" N06 OKL A 401 " ideal model delta sinusoidal sigma weight residual 183.45 47.53 135.92 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 5095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 940 0.037 - 0.074: 265 0.074 - 0.112: 93 0.112 - 0.149: 21 0.149 - 0.186: 4 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA ASN A 110 " pdb=" N ASN A 110 " pdb=" C ASN A 110 " pdb=" CB ASN A 110 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" CA PRO A 31 " pdb=" N PRO A 31 " pdb=" C PRO A 31 " pdb=" CB PRO A 31 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CB THR C 47 " pdb=" CA THR C 47 " pdb=" OG1 THR C 47 " pdb=" CG2 THR C 47 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 1320 not shown) Planarity restraints: 1476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 24 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C ASN D 24 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN D 24 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE D 25 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 167 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO A 168 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 31 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO A 32 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " -0.025 5.00e-02 4.00e+02 ... (remaining 1473 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 337 2.71 - 3.26: 8449 3.26 - 3.80: 13449 3.80 - 4.35: 16469 4.35 - 4.90: 28460 Nonbonded interactions: 67164 Sorted by model distance: nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 175 " model vdw 2.159 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O GLY C 288 " model vdw 2.189 3.040 nonbonded pdb=" O ILE E 138 " pdb=" OG1 THR E 238 " model vdw 2.198 3.040 nonbonded pdb=" O ILE A 278 " pdb=" OG SER A 281 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR C 184 " pdb=" OD2 ASP C 205 " model vdw 2.208 3.040 ... (remaining 67159 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.410 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 22.340 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.004 0.184 8649 Z= 0.201 Angle : 0.612 9.487 11715 Z= 0.317 Chirality : 0.042 0.186 1323 Planarity : 0.004 0.045 1476 Dihedral : 18.046 135.922 3067 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 0.55 % Allowed : 36.50 % Favored : 62.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.26), residues: 1062 helix: 1.73 (0.28), residues: 337 sheet: -1.07 (0.30), residues: 286 loop : -1.40 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 63 HIS 0.004 0.001 HIS C 311 PHE 0.011 0.001 PHE A 197 TYR 0.007 0.001 TYR E 235 ARG 0.003 0.000 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.17031 ( 378) hydrogen bonds : angle 6.42909 ( 1074) SS BOND : bond 0.00521 ( 5) SS BOND : angle 0.99318 ( 10) covalent geometry : bond 0.00415 ( 8644) covalent geometry : angle 0.61194 (11705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 219 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7345 (ttmt) cc_final: 0.7139 (mmtm) REVERT: A 63 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7731 (mmt-90) REVERT: A 288 MET cc_start: 0.7798 (ttm) cc_final: 0.7248 (ttp) REVERT: C 145 TYR cc_start: 0.9107 (p90) cc_final: 0.8734 (p90) REVERT: C 172 GLU cc_start: 0.7195 (pm20) cc_final: 0.6978 (pm20) outliers start: 5 outliers final: 2 residues processed: 221 average time/residue: 0.1992 time to fit residues: 60.3703 Evaluate side-chains 198 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 188 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.0570 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 133 HIS A 134 HIS A 223 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 ASN ** 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 = 0.4141 r_free = 0.4141 target = 0.186840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136037 restraints weight = 10626.927| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.75 r_work: 0.3377 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8649 Z= 0.232 Angle : 0.655 7.191 11715 Z= 0.346 Chirality : 0.045 0.160 1323 Planarity : 0.004 0.046 1476 Dihedral : 6.470 140.056 1169 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 4.26 % Allowed : 32.24 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1062 helix: 1.35 (0.27), residues: 351 sheet: -1.06 (0.31), residues: 265 loop : -1.36 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 47 HIS 0.008 0.001 HIS E 35 PHE 0.015 0.002 PHE A 197 TYR 0.021 0.002 TYR A 284 ARG 0.004 0.000 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 378) hydrogen bonds : angle 5.12980 ( 1074) SS BOND : bond 0.00844 ( 5) SS BOND : angle 1.91400 ( 10) covalent geometry : bond 0.00544 ( 8644) covalent geometry : angle 0.65273 (11705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7502 (ttmt) cc_final: 0.6361 (mtpp) REVERT: A 37 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7888 (mm-30) REVERT: A 63 ARG cc_start: 0.8305 (ttp-110) cc_final: 0.7700 (mmt-90) REVERT: A 66 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8629 (mm) REVERT: A 82 PHE cc_start: 0.8458 (m-80) cc_final: 0.7992 (m-80) REVERT: A 93 TRP cc_start: 0.8383 (t-100) cc_final: 0.7902 (t-100) REVERT: A 97 ASP cc_start: 0.6162 (t0) cc_final: 0.5751 (t0) REVERT: A 137 ASN cc_start: 0.6608 (m-40) cc_final: 0.5934 (m-40) REVERT: A 236 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8456 (t) REVERT: A 269 TYR cc_start: 0.8001 (m-10) cc_final: 0.7771 (m-10) REVERT: A 288 MET cc_start: 0.8342 (ttm) cc_final: 0.8078 (ttp) REVERT: C 246 ASP cc_start: 0.7924 (m-30) cc_final: 0.7624 (m-30) REVERT: E 140 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8460 (ttm) REVERT: E 166 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8239 (tt) outliers start: 39 outliers final: 23 residues processed: 237 average time/residue: 0.1910 time to fit residues: 62.6240 Evaluate side-chains 220 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 68 ASN A 110 ASN B 347 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.189942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139763 restraints weight = 10682.502| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.69 r_work: 0.3431 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8649 Z= 0.140 Angle : 0.579 7.368 11715 Z= 0.304 Chirality : 0.042 0.156 1323 Planarity : 0.004 0.043 1476 Dihedral : 6.050 136.346 1167 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.33 % Rotamer: Outliers : 4.37 % Allowed : 30.93 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1062 helix: 1.53 (0.28), residues: 351 sheet: -0.90 (0.32), residues: 243 loop : -1.34 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 63 HIS 0.005 0.001 HIS E 35 PHE 0.028 0.001 PHE A 38 TYR 0.012 0.001 TYR A 126 ARG 0.003 0.000 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 378) hydrogen bonds : angle 4.71190 ( 1074) SS BOND : bond 0.00666 ( 5) SS BOND : angle 1.62434 ( 10) covalent geometry : bond 0.00320 ( 8644) covalent geometry : angle 0.57776 (11705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8329 (mp) cc_final: 0.8043 (mp) REVERT: A 14 ASP cc_start: 0.8542 (t70) cc_final: 0.8133 (t70) REVERT: A 16 LYS cc_start: 0.7634 (ttmt) cc_final: 0.6718 (mtpp) REVERT: A 21 PHE cc_start: 0.6626 (OUTLIER) cc_final: 0.5664 (m-10) REVERT: A 63 ARG cc_start: 0.8475 (ttp-110) cc_final: 0.7782 (mmt180) REVERT: A 137 ASN cc_start: 0.6815 (m-40) cc_final: 0.6247 (m-40) REVERT: A 167 MET cc_start: 0.5754 (OUTLIER) cc_final: 0.5506 (mmp) REVERT: A 190 GLU cc_start: 0.8429 (mp0) cc_final: 0.7949 (mm-30) REVERT: A 236 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8487 (t) REVERT: A 269 TYR cc_start: 0.7914 (m-10) cc_final: 0.7664 (m-10) REVERT: A 288 MET cc_start: 0.8275 (ttm) cc_final: 0.8065 (ttp) REVERT: C 246 ASP cc_start: 0.7866 (m-30) cc_final: 0.7658 (m-30) REVERT: C 332 TRP cc_start: 0.9038 (m-10) cc_final: 0.8745 (m-10) REVERT: D 48 ASP cc_start: 0.7986 (t0) cc_final: 0.7709 (t0) REVERT: E 140 MET cc_start: 0.8764 (ttm) cc_final: 0.8342 (ttm) REVERT: E 166 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8189 (tt) outliers start: 40 outliers final: 18 residues processed: 233 average time/residue: 0.1800 time to fit residues: 59.2887 Evaluate side-chains 213 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 60 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 141 ASN A 171 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN D 18 GLN ** E 231 GLN ** 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 = 0.4083 r_free = 0.4083 target = 0.180989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129067 restraints weight = 10764.278| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.77 r_work: 0.3307 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 8649 Z= 0.295 Angle : 0.717 8.591 11715 Z= 0.373 Chirality : 0.046 0.175 1323 Planarity : 0.005 0.046 1476 Dihedral : 6.348 129.945 1167 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.93 % Favored : 93.97 % Rotamer: Outliers : 6.56 % Allowed : 29.95 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.25), residues: 1062 helix: 1.38 (0.27), residues: 345 sheet: -1.25 (0.30), residues: 268 loop : -1.47 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 93 HIS 0.010 0.002 HIS E 35 PHE 0.020 0.002 PHE A 197 TYR 0.024 0.002 TYR A 284 ARG 0.004 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 378) hydrogen bonds : angle 5.04666 ( 1074) SS BOND : bond 0.01098 ( 5) SS BOND : angle 2.65583 ( 10) covalent geometry : bond 0.00704 ( 8644) covalent geometry : angle 0.71264 (11705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 197 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7048 (tp30) REVERT: A 16 LYS cc_start: 0.7853 (ttmt) cc_final: 0.7333 (mtpp) REVERT: A 45 ASN cc_start: 0.7952 (m-40) cc_final: 0.7733 (m110) REVERT: A 63 ARG cc_start: 0.8242 (ttp-110) cc_final: 0.7503 (mmt180) REVERT: A 137 ASN cc_start: 0.7238 (m-40) cc_final: 0.6899 (m-40) REVERT: A 167 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5936 (mmp) REVERT: A 192 MET cc_start: 0.7657 (ppp) cc_final: 0.7295 (ppp) REVERT: A 236 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8334 (t) REVERT: A 269 TYR cc_start: 0.8217 (m-10) cc_final: 0.7971 (m-10) REVERT: B 9 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8283 (t0) REVERT: B 188 HIS cc_start: 0.7559 (p90) cc_final: 0.7342 (p-80) REVERT: B 318 GLU cc_start: 0.7317 (mp0) cc_final: 0.7108 (mp0) REVERT: C 117 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8525 (mm) REVERT: C 246 ASP cc_start: 0.8085 (m-30) cc_final: 0.7851 (m-30) REVERT: E 166 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8413 (tt) outliers start: 60 outliers final: 38 residues processed: 236 average time/residue: 0.1770 time to fit residues: 58.9012 Evaluate side-chains 228 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 44 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 171 ASN B 347 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.186684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133224 restraints weight = 10673.575| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.62 r_work: 0.3401 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8649 Z= 0.131 Angle : 0.597 8.607 11715 Z= 0.310 Chirality : 0.042 0.155 1323 Planarity : 0.004 0.051 1476 Dihedral : 6.059 133.272 1167 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.33 % Rotamer: Outliers : 4.37 % Allowed : 33.22 % Favored : 62.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1062 helix: 1.51 (0.27), residues: 355 sheet: -1.11 (0.30), residues: 256 loop : -1.34 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 332 HIS 0.005 0.001 HIS E 35 PHE 0.021 0.001 PHE A 197 TYR 0.012 0.001 TYR E 60 ARG 0.002 0.000 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 378) hydrogen bonds : angle 4.64240 ( 1074) SS BOND : bond 0.00584 ( 5) SS BOND : angle 1.55058 ( 10) covalent geometry : bond 0.00299 ( 8644) covalent geometry : angle 0.59576 (11705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6783 (tp30) REVERT: A 16 LYS cc_start: 0.7876 (ttmt) cc_final: 0.7278 (mtpp) REVERT: A 21 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.5506 (m-10) REVERT: A 63 ARG cc_start: 0.8315 (ttp-110) cc_final: 0.7526 (mmt180) REVERT: A 137 ASN cc_start: 0.7171 (m-40) cc_final: 0.6836 (m-40) REVERT: A 167 MET cc_start: 0.5864 (OUTLIER) cc_final: 0.5534 (mmp) REVERT: A 192 MET cc_start: 0.7919 (ppp) cc_final: 0.7657 (ppp) REVERT: A 196 GLU cc_start: 0.7842 (pt0) cc_final: 0.7612 (pt0) REVERT: A 236 VAL cc_start: 0.8567 (t) cc_final: 0.8258 (t) REVERT: A 255 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7367 (m-10) REVERT: A 269 TYR cc_start: 0.8025 (m-10) cc_final: 0.7768 (m-10) REVERT: A 285 MET cc_start: 0.7618 (ttm) cc_final: 0.7247 (tpp) REVERT: B 9 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7988 (t0) REVERT: B 188 HIS cc_start: 0.7643 (p90) cc_final: 0.7419 (p-80) REVERT: B 318 GLU cc_start: 0.7298 (mp0) cc_final: 0.7068 (mp0) REVERT: C 117 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8326 (mm) REVERT: C 246 ASP cc_start: 0.8042 (m-30) cc_final: 0.7625 (m-30) REVERT: C 301 LYS cc_start: 0.7987 (ptpt) cc_final: 0.7676 (ptmt) REVERT: D 27 ARG cc_start: 0.7315 (mtp-110) cc_final: 0.7085 (mtp-110) REVERT: E 166 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8368 (tt) outliers start: 40 outliers final: 27 residues processed: 221 average time/residue: 0.1831 time to fit residues: 56.9420 Evaluate side-chains 217 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS A 171 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.186654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132594 restraints weight = 10592.673| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.90 r_work: 0.3375 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8649 Z= 0.144 Angle : 0.591 8.404 11715 Z= 0.308 Chirality : 0.042 0.172 1323 Planarity : 0.004 0.052 1476 Dihedral : 5.950 129.523 1167 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 5.25 % Allowed : 32.90 % Favored : 61.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1062 helix: 1.43 (0.27), residues: 355 sheet: -1.05 (0.30), residues: 260 loop : -1.29 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 332 HIS 0.005 0.001 HIS E 35 PHE 0.021 0.001 PHE A 197 TYR 0.011 0.001 TYR E 190 ARG 0.002 0.000 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 378) hydrogen bonds : angle 4.60365 ( 1074) SS BOND : bond 0.00683 ( 5) SS BOND : angle 1.45098 ( 10) covalent geometry : bond 0.00337 ( 8644) covalent geometry : angle 0.58941 (11705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6939 (tm-30) REVERT: A 16 LYS cc_start: 0.7772 (ttmt) cc_final: 0.7051 (mtpp) REVERT: A 21 PHE cc_start: 0.6525 (OUTLIER) cc_final: 0.5484 (m-10) REVERT: A 63 ARG cc_start: 0.8315 (ttp-110) cc_final: 0.7509 (mmt180) REVERT: A 73 ASP cc_start: 0.8292 (t70) cc_final: 0.7670 (t70) REVERT: A 137 ASN cc_start: 0.7251 (m-40) cc_final: 0.6928 (m-40) REVERT: A 167 MET cc_start: 0.5858 (OUTLIER) cc_final: 0.5486 (mmp) REVERT: A 190 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8395 (mp0) REVERT: A 192 MET cc_start: 0.8067 (ppp) cc_final: 0.7815 (ppp) REVERT: A 236 VAL cc_start: 0.8527 (t) cc_final: 0.8196 (t) REVERT: A 255 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7380 (m-10) REVERT: A 269 TYR cc_start: 0.8108 (m-10) cc_final: 0.7768 (m-10) REVERT: B 188 HIS cc_start: 0.7648 (p90) cc_final: 0.7414 (p-80) REVERT: B 318 GLU cc_start: 0.7228 (mp0) cc_final: 0.6999 (mp0) REVERT: C 117 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8263 (mm) REVERT: C 246 ASP cc_start: 0.8134 (m-30) cc_final: 0.7873 (m-30) REVERT: E 166 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8366 (tt) outliers start: 48 outliers final: 32 residues processed: 224 average time/residue: 0.1728 time to fit residues: 54.6474 Evaluate side-chains 216 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 104 optimal weight: 0.0370 chunk 97 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 0.1980 chunk 49 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 77 optimal weight: 40.0000 chunk 46 optimal weight: 0.6980 overall best weight: 1.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 161 HIS A 171 ASN B 347 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.187888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131898 restraints weight = 10784.414| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.99 r_work: 0.3355 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8649 Z= 0.157 Angle : 0.620 8.673 11715 Z= 0.320 Chirality : 0.044 0.272 1323 Planarity : 0.004 0.051 1476 Dihedral : 5.974 129.467 1167 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 6.34 % Allowed : 32.57 % Favored : 61.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1062 helix: 1.39 (0.27), residues: 355 sheet: -1.02 (0.30), residues: 265 loop : -1.27 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 332 HIS 0.006 0.001 HIS E 35 PHE 0.021 0.001 PHE A 38 TYR 0.012 0.001 TYR E 190 ARG 0.002 0.000 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 378) hydrogen bonds : angle 4.62384 ( 1074) SS BOND : bond 0.00709 ( 5) SS BOND : angle 1.43179 ( 10) covalent geometry : bond 0.00370 ( 8644) covalent geometry : angle 0.61860 (11705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8305 (ttp-110) cc_final: 0.7522 (mmt180) REVERT: A 73 ASP cc_start: 0.8461 (t70) cc_final: 0.7877 (t70) REVERT: A 104 LEU cc_start: 0.7907 (mt) cc_final: 0.7496 (mp) REVERT: A 137 ASN cc_start: 0.7274 (m-40) cc_final: 0.6956 (m-40) REVERT: A 167 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.5661 (mmp) REVERT: A 190 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8386 (mp0) REVERT: A 192 MET cc_start: 0.8022 (ppp) cc_final: 0.7729 (ppp) REVERT: A 236 VAL cc_start: 0.8472 (t) cc_final: 0.8146 (t) REVERT: A 255 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7382 (m-10) REVERT: A 269 TYR cc_start: 0.8140 (m-10) cc_final: 0.7894 (m-10) REVERT: A 285 MET cc_start: 0.7652 (ttm) cc_final: 0.7333 (tpp) REVERT: B 188 HIS cc_start: 0.7695 (p90) cc_final: 0.7448 (p-80) REVERT: B 318 GLU cc_start: 0.7193 (mp0) cc_final: 0.6733 (mp0) REVERT: C 117 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8212 (mm) REVERT: C 262 MET cc_start: 0.7163 (ttt) cc_final: 0.6914 (ttt) REVERT: E 166 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8308 (tt) outliers start: 58 outliers final: 41 residues processed: 226 average time/residue: 0.2003 time to fit residues: 63.1516 Evaluate side-chains 227 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 161 HIS ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.185704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.129453 restraints weight = 10745.820| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.76 r_work: 0.3329 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8649 Z= 0.226 Angle : 0.700 10.499 11715 Z= 0.360 Chirality : 0.045 0.205 1323 Planarity : 0.004 0.050 1476 Dihedral : 6.097 127.099 1167 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.44 % Rotamer: Outliers : 6.01 % Allowed : 32.79 % Favored : 61.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1062 helix: 1.28 (0.27), residues: 354 sheet: -1.03 (0.30), residues: 266 loop : -1.31 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 332 HIS 0.018 0.002 HIS A 161 PHE 0.023 0.002 PHE A 197 TYR 0.016 0.002 TYR A 284 ARG 0.002 0.000 ARG E 191 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 378) hydrogen bonds : angle 4.81801 ( 1074) SS BOND : bond 0.01167 ( 5) SS BOND : angle 3.47980 ( 10) covalent geometry : bond 0.00534 ( 8644) covalent geometry : angle 0.69289 (11705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7281 (tm-30) cc_final: 0.7037 (tp30) REVERT: A 63 ARG cc_start: 0.8358 (ttp-110) cc_final: 0.7674 (mmt180) REVERT: A 73 ASP cc_start: 0.8570 (t70) cc_final: 0.7952 (t70) REVERT: A 137 ASN cc_start: 0.7361 (m-40) cc_final: 0.7052 (m-40) REVERT: A 167 MET cc_start: 0.6209 (OUTLIER) cc_final: 0.5729 (mmp) REVERT: A 190 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8375 (mp0) REVERT: A 192 MET cc_start: 0.8116 (ppp) cc_final: 0.7863 (ppp) REVERT: A 236 VAL cc_start: 0.8574 (t) cc_final: 0.8244 (t) REVERT: A 255 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7410 (m-10) REVERT: A 269 TYR cc_start: 0.8097 (m-10) cc_final: 0.7873 (m-10) REVERT: A 285 MET cc_start: 0.7673 (ttm) cc_final: 0.7370 (tpp) REVERT: B 9 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8214 (t0) REVERT: B 188 HIS cc_start: 0.7725 (p90) cc_final: 0.7468 (p-80) REVERT: B 318 GLU cc_start: 0.7228 (mp0) cc_final: 0.6752 (mp0) REVERT: C 117 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8363 (mm) REVERT: E 38 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7948 (ptt-90) REVERT: E 98 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8260 (ptt180) REVERT: E 166 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8410 (tt) outliers start: 55 outliers final: 41 residues processed: 218 average time/residue: 0.1816 time to fit residues: 55.2058 Evaluate side-chains 230 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 8 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 110 ASN A 134 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.186992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131650 restraints weight = 10742.590| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.99 r_work: 0.3361 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8649 Z= 0.157 Angle : 0.656 9.520 11715 Z= 0.339 Chirality : 0.044 0.184 1323 Planarity : 0.004 0.050 1476 Dihedral : 6.023 129.162 1167 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 4.92 % Allowed : 33.77 % Favored : 61.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1062 helix: 1.33 (0.27), residues: 355 sheet: -1.02 (0.30), residues: 260 loop : -1.21 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 332 HIS 0.006 0.001 HIS E 35 PHE 0.038 0.001 PHE A 38 TYR 0.012 0.001 TYR E 60 ARG 0.006 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 378) hydrogen bonds : angle 4.71440 ( 1074) SS BOND : bond 0.00953 ( 5) SS BOND : angle 3.38645 ( 10) covalent geometry : bond 0.00367 ( 8644) covalent geometry : angle 0.64875 (11705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8288 (ttp-110) cc_final: 0.7647 (mmt180) REVERT: A 73 ASP cc_start: 0.8600 (t70) cc_final: 0.7991 (t70) REVERT: A 137 ASN cc_start: 0.7360 (m-40) cc_final: 0.7051 (m-40) REVERT: A 167 MET cc_start: 0.6018 (OUTLIER) cc_final: 0.5552 (mmp) REVERT: A 190 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8314 (mp0) REVERT: A 192 MET cc_start: 0.8110 (ppp) cc_final: 0.7822 (ppp) REVERT: A 236 VAL cc_start: 0.8523 (t) cc_final: 0.8194 (t) REVERT: A 255 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7390 (m-10) REVERT: B 188 HIS cc_start: 0.7761 (p90) cc_final: 0.7511 (p-80) REVERT: B 318 GLU cc_start: 0.7215 (mp0) cc_final: 0.6748 (mp0) REVERT: C 117 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8270 (mm) REVERT: C 301 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7543 (ptmt) REVERT: D 44 HIS cc_start: 0.8502 (m90) cc_final: 0.7898 (m170) REVERT: E 166 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8398 (tt) outliers start: 45 outliers final: 37 residues processed: 212 average time/residue: 0.1870 time to fit residues: 55.2467 Evaluate side-chains 223 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 1 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 0.0070 chunk 40 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 110 ASN A 134 HIS A 161 HIS B 331 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** 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 = 0.4178 r_free = 0.4178 target = 0.191227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138919 restraints weight = 10732.352| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.52 r_work: 0.3415 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8649 Z= 0.141 Angle : 0.669 12.474 11715 Z= 0.342 Chirality : 0.044 0.340 1323 Planarity : 0.004 0.051 1476 Dihedral : 5.971 129.441 1167 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 4.59 % Allowed : 34.54 % Favored : 60.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.25), residues: 1062 helix: 1.34 (0.27), residues: 351 sheet: -0.97 (0.30), residues: 255 loop : -1.19 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 332 HIS 0.005 0.001 HIS A 161 PHE 0.027 0.001 PHE A 40 TYR 0.012 0.001 TYR E 60 ARG 0.005 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 378) hydrogen bonds : angle 4.68758 ( 1074) SS BOND : bond 0.00810 ( 5) SS BOND : angle 3.07405 ( 10) covalent geometry : bond 0.00324 ( 8644) covalent geometry : angle 0.66318 (11705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8388 (ttp-110) cc_final: 0.7821 (mmt180) REVERT: A 73 ASP cc_start: 0.8555 (t70) cc_final: 0.7999 (t70) REVERT: A 137 ASN cc_start: 0.7290 (m-40) cc_final: 0.7041 (m-40) REVERT: A 167 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.5477 (mmp) REVERT: A 192 MET cc_start: 0.8280 (ppp) cc_final: 0.7977 (ppp) REVERT: A 236 VAL cc_start: 0.8810 (t) cc_final: 0.8484 (t) REVERT: A 255 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7238 (m-10) REVERT: B 318 GLU cc_start: 0.7294 (mp0) cc_final: 0.6909 (mp0) REVERT: C 117 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8538 (mm) REVERT: D 21 MET cc_start: 0.7509 (mpp) cc_final: 0.7081 (mpp) REVERT: D 44 HIS cc_start: 0.8431 (m90) cc_final: 0.7970 (m170) REVERT: E 166 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8302 (tt) outliers start: 42 outliers final: 37 residues processed: 214 average time/residue: 0.1805 time to fit residues: 54.3672 Evaluate side-chains 222 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 31 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 103 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 95 optimal weight: 0.0980 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 161 HIS B 188 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.191155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138499 restraints weight = 10889.419| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.56 r_work: 0.3411 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8649 Z= 0.146 Angle : 0.663 11.497 11715 Z= 0.339 Chirality : 0.044 0.358 1323 Planarity : 0.004 0.050 1476 Dihedral : 5.955 129.393 1167 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 4.37 % Allowed : 33.77 % Favored : 61.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.25), residues: 1062 helix: 1.34 (0.27), residues: 352 sheet: -0.90 (0.31), residues: 254 loop : -1.19 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 332 HIS 0.005 0.001 HIS E 35 PHE 0.038 0.001 PHE A 38 TYR 0.030 0.001 TYR A 269 ARG 0.002 0.000 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 378) hydrogen bonds : angle 4.64803 ( 1074) SS BOND : bond 0.00817 ( 5) SS BOND : angle 3.05335 ( 10) covalent geometry : bond 0.00341 ( 8644) covalent geometry : angle 0.65695 (11705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4665.84 seconds wall clock time: 81 minutes 35.04 seconds (4895.04 seconds total)