Starting phenix.real_space_refine on Wed Feb 14 02:45:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7w_35235/02_2024/8i7w_35235_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7w_35235/02_2024/8i7w_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7w_35235/02_2024/8i7w_35235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7w_35235/02_2024/8i7w_35235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7w_35235/02_2024/8i7w_35235_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7w_35235/02_2024/8i7w_35235_updated.pdb" } 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 Residue "A GLU 37": "OE1" <-> "OE2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 73": "OD1" <-> "OD2" Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.81, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 3.05 Conformation dependent library (CDL) restraints added in 1.6 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... running ksdssp... Secondary structure from input PDB file: 19 helices and 15 sheets defined 31.7% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 30 through 53 removed outlier: 4.068A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 88 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 98 through 129 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 141 through 165 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) Processing helix chain 'A' and resid 188 through 217 Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 224 through 259 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 267 through 293 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 7 through 31 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 210 through 216 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) Processing helix chain 'B' and resid 246 through 254 Processing helix chain 'B' and resid 328 through 351 Processing helix chain 'C' and resid 4 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 30 through 34 Processing helix chain 'D' and resid 7 through 21 Processing helix chain 'D' and resid 30 through 44 Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 10 through 12 Processing sheet with id= B, first strand: chain 'A' and resid 169 through 171 Processing sheet with id= C, first strand: chain 'B' and resid 319 through 323 removed outlier: 6.750A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 37 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS B 224 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N HIS B 195 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU B 36 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LYS B 197 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU B 38 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE B 199 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N GLY B 40 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id= D, 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= E, first strand: chain 'C' and resid 100 through 103 removed outlier: 6.984A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 156 through 158 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= G, 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= H, 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: 3.533A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 294 through 296 Processing sheet with id= J, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.745A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS C 337 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing sheet with id= K, 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) Processing sheet with id= L, first strand: chain 'E' and resid 19 through 23 removed outlier: 3.631A pdb=" N LEU E 20 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 115 through 117 removed outlier: 3.560A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.939A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) 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) Processing sheet with id= O, first strand: chain 'E' and resid 155 through 160 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) 346 hydrogen bonds defined for protein. 990 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: 2.21 Time building geometry restraints manager: 3.33 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: 99.21 - 106.33: 175 106.33 - 113.44: 4725 113.44 - 120.55: 3453 120.55 - 127.67: 3264 127.67 - 134.78: 88 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: 8473 3.26 - 3.80: 13479 3.80 - 4.35: 16533 4.35 - 4.90: 28470 Nonbonded interactions: 67292 Sorted by model distance: nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 175 " model vdw 2.159 2.440 nonbonded pdb=" OG1 THR C 274 " pdb=" O GLY C 288 " model vdw 2.189 2.440 nonbonded pdb=" O ILE E 138 " pdb=" OG1 THR E 238 " model vdw 2.198 2.440 nonbonded pdb=" O ILE A 278 " pdb=" OG SER A 281 " model vdw 2.202 2.440 nonbonded pdb=" OG1 THR C 184 " pdb=" OD2 ASP C 205 " model vdw 2.208 2.440 ... (remaining 67287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 2.130 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 25.060 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.060 ------------------------------------------------------------------------------- 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 8644 Z= 0.294 Angle : 0.612 9.487 11705 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 219 time to evaluate : 1.023 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: 0.2032 time to fit residues: 61.5265 Evaluate side-chains 198 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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: 0.2980 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 95 optimal weight: 0.0980 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8644 Z= 0.333 Angle : 0.622 7.014 11705 Z= 0.324 Chirality : 0.044 0.181 1323 Planarity : 0.004 0.047 1476 Dihedral : 6.599 152.732 1169 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.29 % Rotamer: Outliers : 4.37 % Allowed : 33.33 % Favored : 62.30 % 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: -0.67 (0.25), residues: 1062 helix: 1.45 (0.27), residues: 346 sheet: -1.22 (0.31), residues: 267 loop : -1.41 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 0.006 0.000 ARG D 27 *********************** 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 247 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 207 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7550 (ttmt) cc_final: 0.6550 (mtpp) REVERT: A 63 ARG cc_start: 0.8130 (ttp-110) cc_final: 0.7674 (mmt180) REVERT: A 66 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8588 (mm) REVERT: A 82 PHE cc_start: 0.8422 (m-80) cc_final: 0.8015 (m-80) REVERT: A 93 TRP cc_start: 0.8524 (t-100) cc_final: 0.7972 (t-100) REVERT: A 97 ASP cc_start: 0.6547 (t0) cc_final: 0.6340 (t0) REVERT: A 137 ASN cc_start: 0.6557 (m-40) cc_final: 0.6090 (m-40) REVERT: A 236 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8373 (t) REVERT: A 269 TYR cc_start: 0.7835 (m-10) cc_final: 0.7544 (m-10) REVERT: A 288 MET cc_start: 0.7937 (ttm) cc_final: 0.7620 (ttp) outliers start: 40 outliers final: 26 residues processed: 231 average time/residue: 0.1901 time to fit residues: 60.8881 Evaluate side-chains 222 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 194 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 36 LEU 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 119 THR Chi-restraints excluded: chain A residue 182 ILE 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 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 98 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 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 32 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 171 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8644 Z= 0.308 Angle : 0.600 6.841 11705 Z= 0.312 Chirality : 0.043 0.171 1323 Planarity : 0.004 0.045 1476 Dihedral : 5.963 136.308 1165 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 4.26 % Allowed : 32.90 % Favored : 62.84 % 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: -0.61 (0.26), residues: 1062 helix: 1.55 (0.27), residues: 350 sheet: -1.20 (0.30), residues: 271 loop : -1.45 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.008 0.001 HIS E 35 PHE 0.024 0.002 PHE A 38 TYR 0.014 0.002 TYR A 284 ARG 0.003 0.000 ARG A 111 *********************** 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 249 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 210 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7688 (ttmt) cc_final: 0.7051 (mtpp) REVERT: A 37 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7997 (tp30) REVERT: A 63 ARG cc_start: 0.8194 (ttp-110) cc_final: 0.7688 (mmt180) REVERT: A 66 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8653 (mm) REVERT: A 109 MET cc_start: 0.8124 (tmm) cc_final: 0.7865 (tmm) REVERT: A 137 ASN cc_start: 0.6875 (m-40) cc_final: 0.6436 (m-40) REVERT: A 192 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7289 (ppp) REVERT: A 236 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8404 (t) REVERT: A 269 TYR cc_start: 0.7885 (m-10) cc_final: 0.7641 (m-10) REVERT: B 9 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7786 (t0) REVERT: C 246 ASP cc_start: 0.8076 (m-30) cc_final: 0.7832 (m-30) REVERT: C 266 HIS cc_start: 0.5204 (OUTLIER) cc_final: 0.4528 (m90) REVERT: C 333 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8164 (p0) REVERT: D 48 ASP cc_start: 0.8272 (t0) cc_final: 0.8068 (t0) outliers start: 39 outliers final: 27 residues processed: 235 average time/residue: 0.1929 time to fit residues: 62.5847 Evaluate side-chains 226 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 167 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE 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 34 VAL Chi-restraints excluded: chain B residue 222 ILE 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 65 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 333 ASP 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 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 0.0980 chunk 101 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 134 HIS A 171 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8644 Z= 0.178 Angle : 0.564 7.656 11705 Z= 0.292 Chirality : 0.041 0.161 1323 Planarity : 0.003 0.043 1476 Dihedral : 5.853 138.770 1165 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 4.59 % Allowed : 33.66 % Favored : 61.75 % 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: -0.36 (0.26), residues: 1062 helix: 1.90 (0.28), residues: 343 sheet: -0.92 (0.31), residues: 267 loop : -1.50 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 93 HIS 0.005 0.001 HIS A 189 PHE 0.018 0.001 PHE A 197 TYR 0.011 0.001 TYR E 60 ARG 0.004 0.000 ARG A 22 *********************** 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 250 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 208 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8753 (t70) cc_final: 0.8527 (t70) REVERT: A 16 LYS cc_start: 0.7693 (ttmt) cc_final: 0.6999 (mtpp) REVERT: A 21 PHE cc_start: 0.6460 (OUTLIER) cc_final: 0.5538 (m-10) REVERT: A 63 ARG cc_start: 0.8105 (ttp-110) cc_final: 0.7658 (mmt180) REVERT: A 82 PHE cc_start: 0.8426 (m-80) cc_final: 0.8020 (m-80) REVERT: A 109 MET cc_start: 0.8125 (tmm) cc_final: 0.7897 (ttt) REVERT: A 137 ASN cc_start: 0.6786 (m-40) cc_final: 0.6392 (m-40) REVERT: A 167 MET cc_start: 0.5635 (OUTLIER) cc_final: 0.5335 (mmp) REVERT: A 198 PHE cc_start: 0.8727 (m-10) cc_final: 0.8526 (m-10) REVERT: A 269 TYR cc_start: 0.7820 (m-10) cc_final: 0.7559 (m-10) REVERT: C 117 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8436 (mm) REVERT: C 121 CYS cc_start: 0.7002 (t) cc_final: 0.6723 (t) REVERT: C 197 ARG cc_start: 0.7644 (mmp80) cc_final: 0.7378 (tpp-160) REVERT: C 246 ASP cc_start: 0.8021 (m-30) cc_final: 0.7740 (m-30) REVERT: C 266 HIS cc_start: 0.4985 (OUTLIER) cc_final: 0.4435 (m90) REVERT: D 48 ASP cc_start: 0.8068 (t0) cc_final: 0.7807 (t0) outliers start: 42 outliers final: 17 residues processed: 233 average time/residue: 0.1887 time to fit residues: 61.5117 Evaluate side-chains 217 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 29 VAL 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 242 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 222 ILE 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 266 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 25 optimal weight: 30.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8644 Z= 0.379 Angle : 0.654 7.797 11705 Z= 0.340 Chirality : 0.044 0.185 1323 Planarity : 0.004 0.044 1476 Dihedral : 5.998 131.585 1165 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 6.45 % Allowed : 32.24 % 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: -0.55 (0.26), residues: 1062 helix: 1.77 (0.28), residues: 341 sheet: -1.23 (0.30), residues: 278 loop : -1.45 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 47 HIS 0.010 0.001 HIS E 35 PHE 0.021 0.002 PHE A 38 TYR 0.017 0.002 TYR A 284 ARG 0.004 0.000 ARG A 111 *********************** 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 262 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 203 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7810 (mm) cc_final: 0.7384 (mp) REVERT: A 16 LYS cc_start: 0.7511 (ttmt) cc_final: 0.7028 (mtpp) REVERT: A 21 PHE cc_start: 0.6423 (OUTLIER) cc_final: 0.5510 (m-10) REVERT: A 63 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7797 (mmt180) REVERT: A 73 ASP cc_start: 0.8425 (t70) cc_final: 0.7815 (t70) REVERT: A 82 PHE cc_start: 0.8532 (m-80) cc_final: 0.8168 (m-80) REVERT: A 109 MET cc_start: 0.8100 (tmm) cc_final: 0.7859 (ttt) REVERT: A 137 ASN cc_start: 0.7063 (m-40) cc_final: 0.6779 (m-40) REVERT: A 167 MET cc_start: 0.5576 (OUTLIER) cc_final: 0.5253 (mmp) REVERT: A 192 MET cc_start: 0.8053 (ppp) cc_final: 0.7760 (ppp) REVERT: A 236 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8452 (t) REVERT: A 269 TYR cc_start: 0.7908 (m-10) cc_final: 0.7634 (m-10) REVERT: B 9 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7810 (t0) REVERT: B 39 LEU cc_start: 0.6729 (tt) cc_final: 0.6471 (tt) REVERT: C 117 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8582 (mm) REVERT: C 266 HIS cc_start: 0.5294 (OUTLIER) cc_final: 0.4831 (m90) REVERT: D 48 ASP cc_start: 0.8327 (t0) cc_final: 0.8095 (t0) outliers start: 59 outliers final: 40 residues processed: 242 average time/residue: 0.1975 time to fit residues: 66.4004 Evaluate side-chains 236 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 190 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 43 LEU 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 119 THR 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 221 ASP 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 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 342 VAL 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 65 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 296 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 59 optimal weight: 0.2980 chunk 25 optimal weight: 20.0000 chunk 101 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 110 ASN A 134 HIS A 161 HIS A 171 ASN B 188 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8644 Z= 0.196 Angle : 0.593 12.964 11705 Z= 0.306 Chirality : 0.042 0.235 1323 Planarity : 0.003 0.044 1476 Dihedral : 5.831 136.010 1165 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 4.59 % Allowed : 34.43 % Favored : 60.98 % 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: -0.35 (0.26), residues: 1062 helix: 1.79 (0.28), residues: 351 sheet: -0.97 (0.30), residues: 267 loop : -1.40 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.005 0.001 HIS A 161 PHE 0.020 0.001 PHE A 197 TYR 0.017 0.001 TYR E 60 ARG 0.003 0.000 ARG A 22 *********************** 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 248 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 206 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 PHE cc_start: 0.6628 (t80) cc_final: 0.6415 (t80) REVERT: A 11 LEU cc_start: 0.7934 (tp) cc_final: 0.7003 (pp) REVERT: A 16 LYS cc_start: 0.7528 (ttmt) cc_final: 0.6824 (mtpp) REVERT: A 21 PHE cc_start: 0.6300 (OUTLIER) cc_final: 0.5432 (m-10) REVERT: A 63 ARG cc_start: 0.8208 (ttp-110) cc_final: 0.7713 (mmt180) REVERT: A 73 ASP cc_start: 0.8350 (t70) cc_final: 0.7861 (t70) REVERT: A 82 PHE cc_start: 0.8450 (m-80) cc_final: 0.8110 (m-80) REVERT: A 109 MET cc_start: 0.8118 (tmm) cc_final: 0.7843 (ttt) REVERT: A 137 ASN cc_start: 0.7148 (m-40) cc_final: 0.6881 (m-40) REVERT: A 167 MET cc_start: 0.5655 (OUTLIER) cc_final: 0.5180 (mmp) REVERT: A 192 MET cc_start: 0.8035 (ppp) cc_final: 0.7825 (ppp) REVERT: A 236 VAL cc_start: 0.8706 (t) cc_final: 0.8403 (t) REVERT: A 255 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7209 (m-10) REVERT: A 269 TYR cc_start: 0.7896 (m-10) cc_final: 0.7637 (m-10) REVERT: C 117 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8522 (mm) REVERT: C 246 ASP cc_start: 0.8026 (m-30) cc_final: 0.7779 (m-30) REVERT: C 266 HIS cc_start: 0.5255 (OUTLIER) cc_final: 0.4815 (m90) REVERT: D 25 ILE cc_start: 0.7343 (mt) cc_final: 0.6921 (tp) REVERT: D 48 ASP cc_start: 0.8097 (t0) cc_final: 0.7864 (t0) REVERT: E 38 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7763 (ptt-90) outliers start: 42 outliers final: 29 residues processed: 232 average time/residue: 0.1992 time to fit residues: 63.7837 Evaluate side-chains 231 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 196 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 171 ASN 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 B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 35 ASN 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 98 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 296 VAL Chi-restraints excluded: chain E residue 20 LEU 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 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 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 134 HIS A 161 HIS A 171 ASN A 223 HIS ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.005 0.055 8644 Z= 0.356 Angle : 0.669 13.452 11705 Z= 0.343 Chirality : 0.044 0.203 1323 Planarity : 0.004 0.046 1476 Dihedral : 5.876 129.339 1165 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.08 % Favored : 94.82 % Rotamer: Outliers : 6.23 % Allowed : 33.22 % Favored : 60.55 % 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: -0.54 (0.25), residues: 1062 helix: 1.74 (0.28), residues: 341 sheet: -1.18 (0.30), residues: 277 loop : -1.45 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 93 HIS 0.009 0.001 HIS B 188 PHE 0.034 0.002 PHE A 38 TYR 0.015 0.002 TYR E 60 ARG 0.004 0.000 ARG D 27 *********************** 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 250 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 193 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7829 (mm) cc_final: 0.7465 (mp) REVERT: A 16 LYS cc_start: 0.7620 (ttmt) cc_final: 0.6869 (mtpp) REVERT: A 63 ARG cc_start: 0.8288 (ttp-110) cc_final: 0.7671 (mmt180) REVERT: A 73 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8265 (t70) REVERT: A 82 PHE cc_start: 0.8508 (m-80) cc_final: 0.8176 (m-80) REVERT: A 93 TRP cc_start: 0.7965 (t-100) cc_final: 0.7717 (t-100) REVERT: A 109 MET cc_start: 0.8122 (tmm) cc_final: 0.7873 (ttt) REVERT: A 137 ASN cc_start: 0.7217 (m-40) cc_final: 0.6955 (m-40) REVERT: A 167 MET cc_start: 0.5870 (OUTLIER) cc_final: 0.5406 (mmp) REVERT: A 192 MET cc_start: 0.8151 (ppp) cc_final: 0.7936 (ppp) REVERT: A 236 VAL cc_start: 0.8743 (t) cc_final: 0.8417 (t) REVERT: A 255 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7283 (m-10) REVERT: A 269 TYR cc_start: 0.7946 (m-10) cc_final: 0.7713 (m-10) REVERT: B 9 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7851 (t0) REVERT: C 117 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8578 (mm) REVERT: C 217 MET cc_start: 0.7811 (ppp) cc_final: 0.7278 (ptp) REVERT: C 266 HIS cc_start: 0.5286 (OUTLIER) cc_final: 0.4911 (m90) REVERT: C 333 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8200 (p0) REVERT: D 48 ASP cc_start: 0.8304 (t0) cc_final: 0.8071 (t0) REVERT: E 38 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7825 (ptt-90) REVERT: E 83 MET cc_start: 0.7886 (mtt) cc_final: 0.7614 (mtt) outliers start: 57 outliers final: 39 residues processed: 230 average time/residue: 0.1890 time to fit residues: 60.1901 Evaluate side-chains 234 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 187 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 73 ASP 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 119 THR 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 227 LYS 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 188 HIS Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 35 ASN 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 65 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 296 VAL Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 92 optimal weight: 0.0970 chunk 96 optimal weight: 1.9990 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 110 ASN A 134 HIS A 161 HIS A 171 ASN B 188 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8644 Z= 0.232 Angle : 0.633 13.731 11705 Z= 0.324 Chirality : 0.043 0.302 1323 Planarity : 0.004 0.046 1476 Dihedral : 5.840 132.735 1165 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 5.57 % Allowed : 34.32 % Favored : 60.11 % 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: -0.52 (0.25), residues: 1062 helix: 1.58 (0.28), residues: 348 sheet: -1.12 (0.30), residues: 273 loop : -1.36 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.005 0.001 HIS E 35 PHE 0.037 0.001 PHE A 38 TYR 0.016 0.001 TYR E 60 ARG 0.005 0.000 ARG A 111 *********************** 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 250 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 199 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7783 (mm) cc_final: 0.7415 (mp) REVERT: A 16 LYS cc_start: 0.7544 (ttmt) cc_final: 0.6776 (mtpp) REVERT: A 63 ARG cc_start: 0.8256 (ttp-110) cc_final: 0.7668 (mmt180) REVERT: A 73 ASP cc_start: 0.8576 (t70) cc_final: 0.8049 (t70) REVERT: A 82 PHE cc_start: 0.8478 (m-80) cc_final: 0.8131 (m-80) REVERT: A 109 MET cc_start: 0.8002 (tmm) cc_final: 0.7787 (tmm) REVERT: A 137 ASN cc_start: 0.7258 (m-40) cc_final: 0.7013 (m-40) REVERT: A 167 MET cc_start: 0.5794 (OUTLIER) cc_final: 0.5278 (mmp) REVERT: A 192 MET cc_start: 0.8148 (ppp) cc_final: 0.7914 (ppp) REVERT: A 236 VAL cc_start: 0.8732 (t) cc_final: 0.8428 (t) REVERT: A 255 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7241 (m-10) REVERT: A 269 TYR cc_start: 0.7905 (m-10) cc_final: 0.7679 (m-10) REVERT: C 117 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8502 (mm) REVERT: C 246 ASP cc_start: 0.8024 (m-30) cc_final: 0.7766 (m-30) REVERT: C 333 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8149 (p0) REVERT: D 48 ASP cc_start: 0.8158 (t0) cc_final: 0.7918 (t0) REVERT: E 38 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7799 (ptt-90) REVERT: E 83 MET cc_start: 0.7752 (mtt) cc_final: 0.7365 (mtt) outliers start: 51 outliers final: 39 residues processed: 232 average time/residue: 0.1954 time to fit residues: 62.5582 Evaluate side-chains 234 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 190 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 119 THR 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 188 HIS Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 35 ASN 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 65 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 120 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.0030 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 89 optimal weight: 0.0870 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.4968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 134 HIS A 161 HIS A 171 ASN B 188 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8644 Z= 0.189 Angle : 0.629 14.129 11705 Z= 0.321 Chirality : 0.043 0.284 1323 Planarity : 0.003 0.045 1476 Dihedral : 5.804 134.856 1165 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.33 % Rotamer: Outliers : 4.59 % Allowed : 35.85 % Favored : 59.56 % 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: -0.39 (0.25), residues: 1062 helix: 1.68 (0.28), residues: 346 sheet: -0.91 (0.30), residues: 267 loop : -1.38 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 93 HIS 0.005 0.001 HIS B 188 PHE 0.027 0.001 PHE A 40 TYR 0.014 0.001 TYR E 60 ARG 0.004 0.000 ARG A 111 *********************** 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 240 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 198 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7830 (mm) cc_final: 0.7433 (mp) REVERT: A 21 PHE cc_start: 0.6257 (OUTLIER) cc_final: 0.5414 (m-10) REVERT: A 63 ARG cc_start: 0.8233 (ttp-110) cc_final: 0.7649 (mmt180) REVERT: A 73 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.7944 (t70) REVERT: A 137 ASN cc_start: 0.7304 (m-40) cc_final: 0.7068 (m-40) REVERT: A 167 MET cc_start: 0.6092 (OUTLIER) cc_final: 0.5579 (mmp) REVERT: A 192 MET cc_start: 0.8152 (ppp) cc_final: 0.7933 (ppp) REVERT: A 236 VAL cc_start: 0.8765 (t) cc_final: 0.8468 (t) REVERT: A 269 TYR cc_start: 0.7890 (m-10) cc_final: 0.7634 (m-10) REVERT: C 117 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8497 (mm) REVERT: C 217 MET cc_start: 0.7842 (ppp) cc_final: 0.7570 (ppp) REVERT: C 246 ASP cc_start: 0.8014 (m-30) cc_final: 0.7760 (m-30) REVERT: D 44 HIS cc_start: 0.8566 (m90) cc_final: 0.8100 (m-70) REVERT: D 48 ASP cc_start: 0.8074 (t0) cc_final: 0.7802 (t0) REVERT: E 83 MET cc_start: 0.7778 (mtt) cc_final: 0.7535 (mtt) outliers start: 42 outliers final: 33 residues processed: 222 average time/residue: 0.1939 time to fit residues: 59.4211 Evaluate side-chains 227 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 190 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 119 THR 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 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 188 HIS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 35 ASN 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 65 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 120 ILE Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 chunk 104 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 134 HIS A 161 HIS A 171 ASN B 188 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8644 Z= 0.222 Angle : 0.641 13.824 11705 Z= 0.329 Chirality : 0.043 0.254 1323 Planarity : 0.004 0.046 1476 Dihedral : 5.815 133.326 1165 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.81 % Allowed : 34.86 % Favored : 60.33 % 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: -0.35 (0.26), residues: 1062 helix: 1.69 (0.28), residues: 346 sheet: -0.81 (0.30), residues: 267 loop : -1.39 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 93 HIS 0.013 0.001 HIS B 188 PHE 0.040 0.001 PHE A 38 TYR 0.013 0.001 TYR E 60 ARG 0.003 0.000 ARG C 251 ********************** 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 238 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 194 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7641 (mm) cc_final: 0.7373 (mp) REVERT: A 21 PHE cc_start: 0.6212 (OUTLIER) cc_final: 0.5345 (m-10) REVERT: A 63 ARG cc_start: 0.8200 (ttp-110) cc_final: 0.7641 (mmt180) REVERT: A 73 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8008 (t70) REVERT: A 82 PHE cc_start: 0.8354 (m-80) cc_final: 0.8059 (m-80) REVERT: A 137 ASN cc_start: 0.7316 (m-40) cc_final: 0.7087 (m-40) REVERT: A 167 MET cc_start: 0.6141 (OUTLIER) cc_final: 0.5568 (mmp) REVERT: A 192 MET cc_start: 0.8196 (ppp) cc_final: 0.7952 (ppp) REVERT: A 236 VAL cc_start: 0.8685 (t) cc_final: 0.8371 (t) REVERT: A 269 TYR cc_start: 0.7905 (m-10) cc_final: 0.7653 (m-10) REVERT: C 117 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8504 (mm) REVERT: C 197 ARG cc_start: 0.7657 (mmp80) cc_final: 0.7440 (tpp-160) REVERT: C 217 MET cc_start: 0.7846 (ppp) cc_final: 0.7576 (ppp) REVERT: C 246 ASP cc_start: 0.8062 (m-30) cc_final: 0.7779 (m-30) REVERT: C 262 MET cc_start: 0.6935 (ttt) cc_final: 0.6691 (ttt) REVERT: C 325 MET cc_start: 0.7093 (tpp) cc_final: 0.6819 (tpp) REVERT: D 27 ARG cc_start: 0.7035 (mtp-110) cc_final: 0.6459 (ttp-110) REVERT: D 44 HIS cc_start: 0.8588 (m90) cc_final: 0.8116 (m-70) REVERT: D 48 ASP cc_start: 0.8094 (t0) cc_final: 0.7799 (t0) outliers start: 44 outliers final: 37 residues processed: 220 average time/residue: 0.2003 time to fit residues: 61.4947 Evaluate side-chains 230 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 189 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 182 ILE 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 B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 35 ASN 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 65 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 120 ILE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 3.9990 chunk 25 optimal weight: 30.0000 chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 83 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS A 161 HIS A 171 ASN B 188 HIS ** C 32 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 = 0.4145 r_free = 0.4145 target = 0.187193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133203 restraints weight = 10677.678| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.62 r_work: 0.3381 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8644 Z= 0.310 Angle : 0.670 14.096 11705 Z= 0.346 Chirality : 0.044 0.225 1323 Planarity : 0.004 0.047 1476 Dihedral : 5.842 130.938 1165 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.14 % Allowed : 34.54 % Favored : 60.33 % 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: -0.45 (0.26), residues: 1062 helix: 1.63 (0.28), residues: 348 sheet: -1.00 (0.30), residues: 273 loop : -1.38 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 93 HIS 0.008 0.001 HIS E 35 PHE 0.020 0.001 PHE A 197 TYR 0.013 0.001 TYR E 60 ARG 0.003 0.000 ARG A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2243.87 seconds wall clock time: 41 minutes 20.34 seconds (2480.34 seconds total)