Starting phenix.real_space_refine on Tue Feb 13 18:05:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6t_25727/02_2024/7t6t_25727_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6t_25727/02_2024/7t6t_25727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6t_25727/02_2024/7t6t_25727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6t_25727/02_2024/7t6t_25727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6t_25727/02_2024/7t6t_25727_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6t_25727/02_2024/7t6t_25727_neut_updated.pdb" } resolution = 3.2 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= 0.005 sd= 0.052 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: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 4593 2.51 5 N 1216 2.21 5 O 1302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "L PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7164 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2363 Unusual residues: {'PLM': 2} Classifications: {'peptide': 296, 'undetermined': 2} Link IDs: {'PTRANS': 12, 'TRANS': 283, None: 2} Not linked: pdbres="LEU R 316 " pdbres="PLM R 401 " Not linked: pdbres="PLM R 401 " pdbres="PLM R 402 " Time building chain proxies: 4.47, per 1000 atoms: 0.62 Number of scatterers: 7164 At special positions: 0 Unit cell: (87.78, 104.5, 123.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1302 8.00 N 1216 7.00 C 4593 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " 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: 2.95 Conformation dependent library (CDL) restraints added in 1.3 seconds 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 9 sheets defined 42.7% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 10 through 32 Processing helix chain 'A' and resid 43 through 51 removed outlier: 5.818A pdb=" N THR A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.728A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.761A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'R' and resid 24 through 52 removed outlier: 3.637A pdb=" N ILE R 28 " --> pdb=" O PHE R 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR R 29 " --> pdb=" O LEU R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 86 removed outlier: 3.717A pdb=" N PHE R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR R 75 " --> pdb=" O ASP R 71 " (cutoff:3.500A) Proline residue: R 79 - end of helix Processing helix chain 'R' and resid 96 through 128 removed outlier: 4.291A pdb=" N ILE R 116 " --> pdb=" O SER R 112 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 139 through 155 removed outlier: 3.958A pdb=" N ILE R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY R 148 " --> pdb=" O LYS R 144 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 158 through 163 Processing helix chain 'R' and resid 187 through 207 Processing helix chain 'R' and resid 211 through 230 Processing helix chain 'R' and resid 238 through 265 removed outlier: 3.838A pdb=" N ALA R 249 " --> pdb=" O PHE R 245 " (cutoff:3.500A) Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 268 through 271 No H-bonds generated for 'chain 'R' and resid 268 through 271' Processing helix chain 'R' and resid 277 through 301 removed outlier: 3.628A pdb=" N ILE R 281 " --> pdb=" O LYS R 277 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 306 through 315 Processing sheet with id= A, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 223 through 226 Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.808A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.767A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.944A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.792A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.336A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.528A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.585A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) 339 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: 2.25 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1375 1.32 - 1.45: 1754 1.45 - 1.57: 4101 1.57 - 1.69: 0 1.69 - 1.82: 77 Bond restraints: 7307 Sorted by residual: bond pdb=" C LYS C 20 " pdb=" O LYS C 20 " ideal model delta sigma weight residual 1.236 1.291 -0.055 1.19e-02 7.06e+03 2.11e+01 bond pdb=" CA SER R 255 " pdb=" CB SER R 255 " ideal model delta sigma weight residual 1.531 1.474 0.057 1.33e-02 5.65e+03 1.85e+01 bond pdb=" N SER R 181 " pdb=" CA SER R 181 " ideal model delta sigma weight residual 1.458 1.486 -0.028 7.40e-03 1.83e+04 1.47e+01 bond pdb=" N VAL R 127 " pdb=" CA VAL R 127 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.28e+01 bond pdb=" N VAL R 174 " pdb=" CA VAL R 174 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.15e-02 7.56e+03 1.27e+01 ... (remaining 7302 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.97: 157 105.97 - 113.09: 3847 113.09 - 120.21: 3660 120.21 - 127.33: 2154 127.33 - 134.45: 65 Bond angle restraints: 9883 Sorted by residual: angle pdb=" N PRO R 182 " pdb=" CA PRO R 182 " pdb=" C PRO R 182 " ideal model delta sigma weight residual 113.84 104.41 9.43 1.30e+00 5.92e-01 5.26e+01 angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 112.93 106.05 6.88 1.12e+00 7.97e-01 3.78e+01 angle pdb=" N LEU R 300 " pdb=" CA LEU R 300 " pdb=" CB LEU R 300 " ideal model delta sigma weight residual 110.88 102.71 8.17 1.38e+00 5.25e-01 3.51e+01 angle pdb=" N VAL R 266 " pdb=" CA VAL R 266 " pdb=" C VAL R 266 " ideal model delta sigma weight residual 112.83 107.05 5.78 9.90e-01 1.02e+00 3.41e+01 angle pdb=" N MET R 304 " pdb=" CA MET R 304 " pdb=" C MET R 304 " ideal model delta sigma weight residual 112.92 105.86 7.06 1.23e+00 6.61e-01 3.29e+01 ... (remaining 9878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 3909 16.92 - 33.85: 333 33.85 - 50.77: 80 50.77 - 67.69: 13 67.69 - 84.62: 3 Dihedral angle restraints: 4338 sinusoidal: 1709 harmonic: 2629 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual 93.00 177.62 -84.62 1 1.00e+01 1.00e-02 8.70e+01 dihedral pdb=" C PHE R 178 " pdb=" N PHE R 178 " pdb=" CA PHE R 178 " pdb=" CB PHE R 178 " ideal model delta harmonic sigma weight residual -122.60 -112.55 -10.05 0 2.50e+00 1.60e-01 1.62e+01 dihedral pdb=" C GLU R 189 " pdb=" N GLU R 189 " pdb=" CA GLU R 189 " pdb=" CB GLU R 189 " ideal model delta harmonic sigma weight residual -122.60 -132.08 9.48 0 2.50e+00 1.60e-01 1.44e+01 ... (remaining 4335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 532 0.070 - 0.140: 398 0.140 - 0.211: 169 0.211 - 0.281: 34 0.281 - 0.351: 4 Chirality restraints: 1137 Sorted by residual: chirality pdb=" CA PHE B 235 " pdb=" N PHE B 235 " pdb=" C PHE B 235 " pdb=" CB PHE B 235 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA PHE R 178 " pdb=" N PHE R 178 " pdb=" C PHE R 178 " pdb=" CB PHE R 178 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1134 not shown) Planarity restraints: 1241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N FME L 1 " 0.057 2.00e-02 2.50e+03 7.27e-02 5.28e+01 pdb=" CA FME L 1 " -0.064 2.00e-02 2.50e+03 pdb=" CN FME L 1 " 0.086 2.00e-02 2.50e+03 pdb=" O1 FME L 1 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 24 " -0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C ASN C 24 " 0.079 2.00e-02 2.50e+03 pdb=" O ASN C 24 " -0.029 2.00e-02 2.50e+03 pdb=" N ILE C 25 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 19 " 0.022 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C LEU C 19 " -0.074 2.00e-02 2.50e+03 pdb=" O LEU C 19 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS C 20 " 0.025 2.00e-02 2.50e+03 ... (remaining 1238 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 973 2.76 - 3.29: 7537 3.29 - 3.83: 11826 3.83 - 4.36: 15397 4.36 - 4.90: 25456 Nonbonded interactions: 61189 Sorted by model distance: nonbonded pdb=" OD1 ASN B 313 " pdb=" N ARG B 314 " model vdw 2.223 2.520 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.232 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.279 2.440 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.339 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.350 2.440 ... (remaining 61184 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: 0.400 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: 2.090 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.810 Find NCS groups from input model: 0.210 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 : 0.011 0.075 7307 Z= 0.745 Angle : 1.550 9.431 9883 Z= 1.170 Chirality : 0.105 0.351 1137 Planarity : 0.008 0.073 1241 Dihedral : 13.221 78.320 2629 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.16 % Allowed : 5.68 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.27), residues: 893 helix: 1.10 (0.25), residues: 395 sheet: -0.77 (0.38), residues: 178 loop : -0.42 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP R 132 HIS 0.012 0.002 HIS B 54 PHE 0.013 0.002 PHE R 110 TYR 0.013 0.002 TYR C 40 ARG 0.005 0.001 ARG R 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 293 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8017 (p0) cc_final: 0.7781 (p0) REVERT: A 38 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8012 (tt) REVERT: A 251 ASP cc_start: 0.7989 (t0) cc_final: 0.7697 (t0) REVERT: A 252 SER cc_start: 0.8868 (t) cc_final: 0.8664 (t) REVERT: A 262 THR cc_start: 0.9096 (m) cc_final: 0.8782 (p) REVERT: A 276 GLU cc_start: 0.7594 (mp0) cc_final: 0.6575 (mp0) REVERT: A 280 LYS cc_start: 0.8507 (mptt) cc_final: 0.8092 (mptt) REVERT: A 296 TYR cc_start: 0.8746 (t80) cc_final: 0.8131 (t80) REVERT: A 312 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8329 (mmmt) REVERT: A 321 THR cc_start: 0.8481 (m) cc_final: 0.8196 (p) REVERT: B 13 GLN cc_start: 0.8188 (tt0) cc_final: 0.7962 (tt0) REVERT: B 19 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7693 (ttp80) REVERT: B 50 THR cc_start: 0.8206 (m) cc_final: 0.8006 (t) REVERT: B 175 GLN cc_start: 0.7949 (pp30) cc_final: 0.7548 (pp30) REVERT: B 176 GLN cc_start: 0.8405 (mt0) cc_final: 0.7794 (mt0) REVERT: B 189 SER cc_start: 0.8737 (p) cc_final: 0.8491 (p) REVERT: B 212 ASP cc_start: 0.7385 (m-30) cc_final: 0.7167 (t0) REVERT: B 225 HIS cc_start: 0.8517 (m-70) cc_final: 0.8283 (m-70) REVERT: B 243 THR cc_start: 0.8572 (m) cc_final: 0.8211 (p) REVERT: B 247 ASP cc_start: 0.8079 (p0) cc_final: 0.7822 (p0) REVERT: B 258 ASP cc_start: 0.7620 (t0) cc_final: 0.7114 (t0) REVERT: B 333 ASP cc_start: 0.7086 (p0) cc_final: 0.6852 (p0) REVERT: C 18 GLN cc_start: 0.8152 (tp-100) cc_final: 0.7705 (tp40) REVERT: R 63 SER cc_start: 0.8003 (m) cc_final: 0.7765 (p) REVERT: R 80 PHE cc_start: 0.8520 (m-80) cc_final: 0.8246 (m-80) REVERT: R 190 ARG cc_start: 0.8510 (ttp80) cc_final: 0.8236 (ttp-170) REVERT: R 207 ILE cc_start: 0.8840 (pt) cc_final: 0.8514 (mm) REVERT: R 265 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8106 (p) REVERT: R 277 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8548 (mmmt) REVERT: R 294 SER cc_start: 0.8550 (m) cc_final: 0.8279 (t) REVERT: R 302 VAL cc_start: 0.8408 (m) cc_final: 0.8039 (t) outliers start: 9 outliers final: 1 residues processed: 295 average time/residue: 0.2243 time to fit residues: 83.7744 Evaluate side-chains 257 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 254 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain R residue 265 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS R 57 HIS R 231 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7307 Z= 0.218 Angle : 0.582 6.872 9883 Z= 0.315 Chirality : 0.044 0.200 1137 Planarity : 0.004 0.049 1241 Dihedral : 5.748 49.273 1006 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.97 % Allowed : 16.93 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.27), residues: 893 helix: 0.96 (0.25), residues: 396 sheet: -0.39 (0.38), residues: 171 loop : -0.67 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.004 0.001 HIS B 54 PHE 0.020 0.002 PHE R 178 TYR 0.015 0.002 TYR B 59 ARG 0.007 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 261 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7960 (p0) cc_final: 0.7753 (p0) REVERT: A 251 ASP cc_start: 0.7990 (t0) cc_final: 0.7739 (t0) REVERT: A 262 THR cc_start: 0.9012 (m) cc_final: 0.8658 (p) REVERT: A 279 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8418 (mtpp) REVERT: A 280 LYS cc_start: 0.8529 (mptt) cc_final: 0.7836 (mptt) REVERT: A 296 TYR cc_start: 0.8789 (t80) cc_final: 0.8201 (t80) REVERT: A 312 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8352 (mmmt) REVERT: A 321 THR cc_start: 0.8347 (m) cc_final: 0.7994 (p) REVERT: B 19 ARG cc_start: 0.7944 (ttp-110) cc_final: 0.7700 (ttp80) REVERT: B 29 THR cc_start: 0.8178 (p) cc_final: 0.7746 (t) REVERT: B 130 GLU cc_start: 0.4947 (tp30) cc_final: 0.4556 (tp30) REVERT: B 175 GLN cc_start: 0.8023 (pp30) cc_final: 0.7702 (pp30) REVERT: B 176 GLN cc_start: 0.8329 (mt0) cc_final: 0.7648 (mt0) REVERT: B 189 SER cc_start: 0.8649 (p) cc_final: 0.8290 (p) REVERT: B 225 HIS cc_start: 0.8479 (m-70) cc_final: 0.8214 (m-70) REVERT: B 247 ASP cc_start: 0.7997 (p0) cc_final: 0.7796 (p0) REVERT: B 258 ASP cc_start: 0.7588 (t0) cc_final: 0.6891 (t0) REVERT: B 333 ASP cc_start: 0.7040 (p0) cc_final: 0.6839 (p0) REVERT: C 21 MET cc_start: 0.7193 (mmm) cc_final: 0.6535 (mmm) REVERT: R 65 LEU cc_start: 0.8718 (tp) cc_final: 0.8506 (tp) REVERT: R 197 MET cc_start: 0.7770 (mmp) cc_final: 0.7470 (mmt) REVERT: R 207 ILE cc_start: 0.8785 (pt) cc_final: 0.8496 (mm) REVERT: R 215 SER cc_start: 0.8436 (t) cc_final: 0.8229 (p) REVERT: R 277 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8471 (mmmt) REVERT: R 294 SER cc_start: 0.8437 (m) cc_final: 0.8227 (t) outliers start: 23 outliers final: 11 residues processed: 267 average time/residue: 0.2264 time to fit residues: 77.1251 Evaluate side-chains 273 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 261 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 296 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 57 HIS R 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7307 Z= 0.217 Angle : 0.545 7.004 9883 Z= 0.290 Chirality : 0.043 0.199 1137 Planarity : 0.004 0.047 1241 Dihedral : 5.392 47.481 1003 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.13 % Allowed : 19.25 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.28), residues: 893 helix: 0.89 (0.26), residues: 399 sheet: -0.41 (0.39), residues: 169 loop : -0.81 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.021 0.002 PHE A 334 TYR 0.016 0.001 TYR B 124 ARG 0.008 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 265 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7945 (t0) cc_final: 0.7713 (t0) REVERT: A 279 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8612 (mtmt) REVERT: A 280 LYS cc_start: 0.8547 (mptt) cc_final: 0.8279 (mptt) REVERT: A 296 TYR cc_start: 0.8842 (t80) cc_final: 0.8347 (t80) REVERT: A 312 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8375 (mmmt) REVERT: A 321 THR cc_start: 0.8315 (m) cc_final: 0.7923 (p) REVERT: B 10 GLU cc_start: 0.8951 (tp30) cc_final: 0.8623 (tp30) REVERT: B 105 TYR cc_start: 0.8677 (t80) cc_final: 0.8296 (t80) REVERT: B 156 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7342 (mt0) REVERT: B 189 SER cc_start: 0.8618 (p) cc_final: 0.8409 (p) REVERT: B 217 MET cc_start: 0.7795 (ppp) cc_final: 0.7510 (ppp) REVERT: B 291 ASP cc_start: 0.7634 (t0) cc_final: 0.7268 (t0) REVERT: B 311 HIS cc_start: 0.7386 (m-70) cc_final: 0.7132 (m-70) REVERT: R 33 PHE cc_start: 0.8617 (m-80) cc_final: 0.8118 (m-80) REVERT: R 39 LEU cc_start: 0.8552 (mm) cc_final: 0.8341 (mm) REVERT: R 77 THR cc_start: 0.8145 (m) cc_final: 0.7800 (p) REVERT: R 190 ARG cc_start: 0.8398 (tmm160) cc_final: 0.8180 (tmm160) REVERT: R 197 MET cc_start: 0.7789 (mmp) cc_final: 0.7497 (mmt) REVERT: R 267 ARG cc_start: 0.8180 (mmt90) cc_final: 0.7736 (mtp85) REVERT: R 277 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8394 (mmmt) REVERT: R 294 SER cc_start: 0.8465 (m) cc_final: 0.8219 (t) REVERT: R 309 ARG cc_start: 0.8063 (ttm110) cc_final: 0.7555 (mtm110) outliers start: 32 outliers final: 18 residues processed: 277 average time/residue: 0.2368 time to fit residues: 82.3103 Evaluate side-chains 272 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 253 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 189 GLU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 302 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN R 57 HIS R 129 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7307 Z= 0.298 Angle : 0.566 8.265 9883 Z= 0.302 Chirality : 0.044 0.156 1137 Planarity : 0.004 0.045 1241 Dihedral : 5.523 46.130 1003 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.52 % Allowed : 22.35 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.28), residues: 893 helix: 0.74 (0.26), residues: 400 sheet: -0.37 (0.39), residues: 169 loop : -0.86 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.020 0.002 PHE A 334 TYR 0.013 0.001 TYR B 124 ARG 0.009 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 265 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8607 (mtmt) REVERT: A 280 LYS cc_start: 0.8583 (mptt) cc_final: 0.8304 (mptt) REVERT: A 296 TYR cc_start: 0.8908 (t80) cc_final: 0.8484 (t80) REVERT: A 312 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8428 (mmmt) REVERT: A 321 THR cc_start: 0.8348 (m) cc_final: 0.7997 (p) REVERT: B 105 TYR cc_start: 0.8698 (t80) cc_final: 0.8335 (t80) REVERT: B 189 SER cc_start: 0.8628 (p) cc_final: 0.8409 (p) REVERT: B 217 MET cc_start: 0.7770 (ppp) cc_final: 0.7522 (ppp) REVERT: B 291 ASP cc_start: 0.7695 (t0) cc_final: 0.7166 (t0) REVERT: R 77 THR cc_start: 0.8169 (m) cc_final: 0.7846 (p) REVERT: R 197 MET cc_start: 0.7807 (mmp) cc_final: 0.7484 (mmt) REVERT: R 243 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7934 (mm) REVERT: R 267 ARG cc_start: 0.8162 (mmt90) cc_final: 0.7778 (mtp85) REVERT: R 277 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8458 (mmmt) REVERT: R 294 SER cc_start: 0.8483 (m) cc_final: 0.8237 (t) outliers start: 35 outliers final: 29 residues processed: 274 average time/residue: 0.2564 time to fit residues: 88.1129 Evaluate side-chains 287 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 256 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain R residue 302 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 57 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7307 Z= 0.218 Angle : 0.545 9.042 9883 Z= 0.289 Chirality : 0.043 0.168 1137 Planarity : 0.004 0.043 1241 Dihedral : 5.422 49.030 1003 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.26 % Allowed : 24.03 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.28), residues: 893 helix: 0.78 (0.26), residues: 399 sheet: -0.27 (0.39), residues: 169 loop : -0.92 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.002 0.001 HIS B 183 PHE 0.022 0.001 PHE A 334 TYR 0.014 0.001 TYR B 124 ARG 0.010 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 258 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8621 (mtmt) REVERT: A 280 LYS cc_start: 0.8587 (mptt) cc_final: 0.8292 (mptt) REVERT: A 296 TYR cc_start: 0.8908 (t80) cc_final: 0.8508 (t80) REVERT: A 312 LYS cc_start: 0.8697 (mmmt) cc_final: 0.8450 (mmmt) REVERT: A 321 THR cc_start: 0.8347 (m) cc_final: 0.7985 (p) REVERT: B 105 TYR cc_start: 0.8676 (t80) cc_final: 0.8354 (t80) REVERT: B 189 SER cc_start: 0.8568 (p) cc_final: 0.8346 (p) REVERT: B 217 MET cc_start: 0.7753 (ppp) cc_final: 0.7553 (ptm) REVERT: B 243 THR cc_start: 0.8503 (t) cc_final: 0.8296 (p) REVERT: B 291 ASP cc_start: 0.7830 (t0) cc_final: 0.7329 (t0) REVERT: R 25 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8275 (mp) REVERT: R 33 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7526 (t80) REVERT: R 77 THR cc_start: 0.8148 (m) cc_final: 0.7853 (p) REVERT: R 163 ARG cc_start: 0.8597 (mmm160) cc_final: 0.8373 (mmp80) REVERT: R 197 MET cc_start: 0.7748 (mmp) cc_final: 0.7465 (mmt) REVERT: R 226 THR cc_start: 0.8286 (p) cc_final: 0.8019 (t) REVERT: R 243 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7936 (mm) REVERT: R 267 ARG cc_start: 0.8129 (mmt90) cc_final: 0.7721 (mtp85) REVERT: R 277 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8440 (mmmt) REVERT: R 294 SER cc_start: 0.8560 (m) cc_final: 0.8308 (t) REVERT: R 309 ARG cc_start: 0.8053 (ttm110) cc_final: 0.7776 (mtm110) outliers start: 33 outliers final: 24 residues processed: 268 average time/residue: 0.2425 time to fit residues: 81.5311 Evaluate side-chains 281 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 253 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 33 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 302 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7307 Z= 0.192 Angle : 0.550 10.547 9883 Z= 0.287 Chirality : 0.042 0.173 1137 Planarity : 0.004 0.050 1241 Dihedral : 5.281 49.621 1003 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.78 % Allowed : 24.42 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.28), residues: 893 helix: 0.88 (0.26), residues: 399 sheet: -0.10 (0.40), residues: 169 loop : -0.85 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS B 183 PHE 0.023 0.001 PHE A 334 TYR 0.012 0.001 TYR B 124 ARG 0.012 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 255 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8025 (mmtm) cc_final: 0.7471 (mmtm) REVERT: A 279 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8646 (mtmt) REVERT: A 280 LYS cc_start: 0.8578 (mptt) cc_final: 0.8277 (mptt) REVERT: A 296 TYR cc_start: 0.8920 (t80) cc_final: 0.8514 (t80) REVERT: A 312 LYS cc_start: 0.8738 (mmmt) cc_final: 0.8484 (mmmt) REVERT: A 321 THR cc_start: 0.8375 (m) cc_final: 0.7981 (p) REVERT: A 324 THR cc_start: 0.7521 (p) cc_final: 0.7296 (p) REVERT: B 189 SER cc_start: 0.8565 (p) cc_final: 0.8358 (p) REVERT: B 217 MET cc_start: 0.7752 (ppp) cc_final: 0.7552 (ptm) REVERT: B 228 ASP cc_start: 0.6345 (OUTLIER) cc_final: 0.6097 (t0) REVERT: B 291 ASP cc_start: 0.7832 (t0) cc_final: 0.7316 (t0) REVERT: R 33 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.7566 (t80) REVERT: R 77 THR cc_start: 0.8161 (m) cc_final: 0.7859 (p) REVERT: R 82 MET cc_start: 0.7024 (mpp) cc_final: 0.6058 (mpp) REVERT: R 100 PHE cc_start: 0.8475 (t80) cc_final: 0.8138 (t80) REVERT: R 197 MET cc_start: 0.7761 (mmp) cc_final: 0.7422 (mmt) REVERT: R 226 THR cc_start: 0.8210 (p) cc_final: 0.7973 (t) REVERT: R 243 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7923 (mm) REVERT: R 258 GLN cc_start: 0.7667 (tp40) cc_final: 0.7460 (tp40) REVERT: R 267 ARG cc_start: 0.8091 (mmt90) cc_final: 0.7683 (mtp85) REVERT: R 277 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8379 (mmmt) REVERT: R 294 SER cc_start: 0.8538 (m) cc_final: 0.8302 (t) REVERT: R 309 ARG cc_start: 0.8033 (ttm110) cc_final: 0.7742 (mtm110) outliers start: 37 outliers final: 25 residues processed: 271 average time/residue: 0.2411 time to fit residues: 82.1815 Evaluate side-chains 280 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 251 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 33 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain R residue 304 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 84 optimal weight: 0.0470 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7307 Z= 0.307 Angle : 0.587 12.239 9883 Z= 0.307 Chirality : 0.044 0.172 1137 Planarity : 0.004 0.040 1241 Dihedral : 5.507 55.855 1003 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.68 % Allowed : 24.42 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.28), residues: 893 helix: 0.84 (0.26), residues: 397 sheet: -0.21 (0.39), residues: 169 loop : -0.92 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.003 0.001 HIS B 183 PHE 0.018 0.002 PHE R 178 TYR 0.010 0.001 TYR B 59 ARG 0.010 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 259 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 TYR cc_start: 0.8968 (t80) cc_final: 0.8647 (t80) REVERT: A 312 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8531 (mmmt) REVERT: A 321 THR cc_start: 0.8391 (m) cc_final: 0.8002 (p) REVERT: A 324 THR cc_start: 0.7581 (p) cc_final: 0.7358 (p) REVERT: B 189 SER cc_start: 0.8589 (p) cc_final: 0.8372 (p) REVERT: B 291 ASP cc_start: 0.7927 (t0) cc_final: 0.7421 (t0) REVERT: C 52 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8251 (p) REVERT: R 25 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8311 (mp) REVERT: R 33 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.7424 (t80) REVERT: R 82 MET cc_start: 0.7059 (mpp) cc_final: 0.6312 (mpp) REVERT: R 197 MET cc_start: 0.7750 (mmp) cc_final: 0.7539 (mmt) REVERT: R 243 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7935 (mm) REVERT: R 258 GLN cc_start: 0.7761 (tp40) cc_final: 0.7495 (tp40) REVERT: R 267 ARG cc_start: 0.8140 (mmt90) cc_final: 0.7731 (mtp85) REVERT: R 277 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8415 (mmmt) REVERT: R 294 SER cc_start: 0.8605 (m) cc_final: 0.8345 (t) REVERT: R 309 ARG cc_start: 0.8039 (ttm110) cc_final: 0.7723 (mtm110) outliers start: 44 outliers final: 32 residues processed: 274 average time/residue: 0.2390 time to fit residues: 82.3302 Evaluate side-chains 288 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 252 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 33 PHE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain R residue 304 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN R 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7307 Z= 0.300 Angle : 0.594 11.043 9883 Z= 0.310 Chirality : 0.044 0.186 1137 Planarity : 0.004 0.038 1241 Dihedral : 5.473 42.569 1003 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 5.81 % Allowed : 25.32 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.28), residues: 893 helix: 0.76 (0.26), residues: 398 sheet: -0.26 (0.39), residues: 169 loop : -0.97 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.024 0.002 PHE A 334 TYR 0.013 0.001 TYR B 124 ARG 0.008 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 259 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.8342 (tp-100) cc_final: 0.7954 (tp-100) REVERT: A 210 LYS cc_start: 0.7973 (mmtm) cc_final: 0.7269 (mmtm) REVERT: A 279 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8135 (mtmt) REVERT: A 296 TYR cc_start: 0.8925 (t80) cc_final: 0.8606 (t80) REVERT: A 309 ASP cc_start: 0.7351 (m-30) cc_final: 0.6983 (m-30) REVERT: A 312 LYS cc_start: 0.8825 (mmmt) cc_final: 0.8550 (mmmt) REVERT: A 321 THR cc_start: 0.8441 (m) cc_final: 0.8055 (p) REVERT: A 324 THR cc_start: 0.7607 (p) cc_final: 0.7371 (p) REVERT: B 61 MET cc_start: 0.7469 (ppp) cc_final: 0.7205 (ppp) REVERT: B 189 SER cc_start: 0.8593 (p) cc_final: 0.8389 (p) REVERT: B 255 LEU cc_start: 0.8614 (mm) cc_final: 0.8381 (mt) REVERT: B 291 ASP cc_start: 0.8015 (t0) cc_final: 0.7519 (t0) REVERT: B 301 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8545 (mmmt) REVERT: R 25 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8312 (mp) REVERT: R 100 PHE cc_start: 0.8422 (t80) cc_final: 0.8160 (t80) REVERT: R 243 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7942 (mm) REVERT: R 258 GLN cc_start: 0.7791 (tp40) cc_final: 0.7539 (tp40) REVERT: R 267 ARG cc_start: 0.8129 (mmt90) cc_final: 0.7733 (mtp85) REVERT: R 277 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8546 (mmmt) REVERT: R 294 SER cc_start: 0.8604 (m) cc_final: 0.8350 (t) REVERT: R 309 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7718 (mtm110) outliers start: 45 outliers final: 36 residues processed: 276 average time/residue: 0.2309 time to fit residues: 80.3619 Evaluate side-chains 295 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 256 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain R residue 304 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7307 Z= 0.233 Angle : 0.598 13.360 9883 Z= 0.307 Chirality : 0.043 0.180 1137 Planarity : 0.004 0.038 1241 Dihedral : 5.368 45.254 1003 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.52 % Allowed : 27.00 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.28), residues: 893 helix: 0.78 (0.27), residues: 398 sheet: -0.21 (0.39), residues: 164 loop : -0.97 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS B 183 PHE 0.021 0.002 PHE A 334 TYR 0.012 0.001 TYR B 124 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 254 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7926 (tp-100) REVERT: A 279 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8132 (mtmt) REVERT: A 296 TYR cc_start: 0.8904 (t80) cc_final: 0.8601 (t80) REVERT: A 309 ASP cc_start: 0.7317 (m-30) cc_final: 0.6953 (m-30) REVERT: A 312 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8540 (mmmt) REVERT: A 321 THR cc_start: 0.8409 (m) cc_final: 0.7996 (p) REVERT: A 324 THR cc_start: 0.7521 (p) cc_final: 0.7289 (p) REVERT: B 8 ARG cc_start: 0.7288 (mpt180) cc_final: 0.6409 (mtm-85) REVERT: B 61 MET cc_start: 0.7483 (ppp) cc_final: 0.7235 (ppp) REVERT: B 111 TYR cc_start: 0.8178 (m-80) cc_final: 0.7967 (m-80) REVERT: B 189 SER cc_start: 0.8565 (p) cc_final: 0.8354 (p) REVERT: B 291 ASP cc_start: 0.7980 (t0) cc_final: 0.7523 (t0) REVERT: C 18 GLN cc_start: 0.8148 (tp40) cc_final: 0.7796 (tp40) REVERT: R 25 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8292 (mp) REVERT: R 33 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.7495 (t80) REVERT: R 82 MET cc_start: 0.7161 (mpp) cc_final: 0.6227 (mpp) REVERT: R 100 PHE cc_start: 0.8380 (t80) cc_final: 0.8113 (t80) REVERT: R 243 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7896 (mm) REVERT: R 267 ARG cc_start: 0.8031 (mmt90) cc_final: 0.7638 (mtp85) REVERT: R 277 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8467 (mmmt) REVERT: R 294 SER cc_start: 0.8588 (m) cc_final: 0.8341 (t) REVERT: R 309 ARG cc_start: 0.8027 (ttm110) cc_final: 0.7725 (mtm110) outliers start: 35 outliers final: 27 residues processed: 269 average time/residue: 0.2446 time to fit residues: 82.9660 Evaluate side-chains 284 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 253 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 33 PHE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 302 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 0.0060 chunk 87 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN R 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7307 Z= 0.304 Angle : 0.636 12.417 9883 Z= 0.328 Chirality : 0.044 0.174 1137 Planarity : 0.004 0.038 1241 Dihedral : 5.506 57.179 1003 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.13 % Allowed : 26.87 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.28), residues: 893 helix: 0.71 (0.27), residues: 399 sheet: -0.29 (0.39), residues: 165 loop : -0.94 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS B 183 PHE 0.020 0.002 PHE A 334 TYR 0.011 0.001 TYR B 124 ARG 0.008 0.001 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 260 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.8352 (tp-100) cc_final: 0.7958 (tp-100) REVERT: A 210 LYS cc_start: 0.8317 (mtpp) cc_final: 0.7883 (mmtm) REVERT: A 279 LYS cc_start: 0.8890 (mtmt) cc_final: 0.8165 (mtmt) REVERT: A 296 TYR cc_start: 0.8884 (t80) cc_final: 0.8585 (t80) REVERT: A 309 ASP cc_start: 0.7344 (m-30) cc_final: 0.7008 (m-30) REVERT: A 312 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8502 (mmmt) REVERT: A 321 THR cc_start: 0.8424 (m) cc_final: 0.8032 (p) REVERT: A 324 THR cc_start: 0.7566 (p) cc_final: 0.7358 (p) REVERT: B 8 ARG cc_start: 0.7363 (mpt180) cc_final: 0.6713 (mtm-85) REVERT: B 61 MET cc_start: 0.7452 (ppp) cc_final: 0.7232 (ppp) REVERT: B 189 SER cc_start: 0.8598 (p) cc_final: 0.8374 (p) REVERT: B 291 ASP cc_start: 0.7949 (t0) cc_final: 0.7629 (t0) REVERT: C 18 GLN cc_start: 0.8165 (tp40) cc_final: 0.7803 (tp40) REVERT: R 25 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8314 (mp) REVERT: R 33 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.7519 (t80) REVERT: R 82 MET cc_start: 0.7151 (mpp) cc_final: 0.6176 (mpp) REVERT: R 100 PHE cc_start: 0.8419 (t80) cc_final: 0.8125 (t80) REVERT: R 243 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7952 (mm) REVERT: R 267 ARG cc_start: 0.8061 (mmt90) cc_final: 0.7670 (mtp85) REVERT: R 277 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8464 (mmmt) REVERT: R 294 SER cc_start: 0.8604 (m) cc_final: 0.8367 (t) REVERT: R 309 ARG cc_start: 0.8101 (ttm110) cc_final: 0.7804 (mtm110) outliers start: 32 outliers final: 27 residues processed: 274 average time/residue: 0.2424 time to fit residues: 83.4234 Evaluate side-chains 288 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 258 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 33 PHE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 302 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.105049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.092426 restraints weight = 12831.672| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.60 r_work: 0.3182 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7307 Z= 0.236 Angle : 0.618 13.020 9883 Z= 0.315 Chirality : 0.043 0.169 1137 Planarity : 0.004 0.037 1241 Dihedral : 5.370 54.271 1003 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.39 % Allowed : 26.74 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.28), residues: 893 helix: 0.82 (0.27), residues: 399 sheet: -0.24 (0.39), residues: 170 loop : -0.88 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 183 PHE 0.039 0.002 PHE R 74 TYR 0.012 0.001 TYR B 124 ARG 0.009 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2191.17 seconds wall clock time: 40 minutes 28.42 seconds (2428.42 seconds total)