Starting phenix.real_space_refine on Thu Feb 13 11:20:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vms_21243/02_2025/6vms_21243.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vms_21243/02_2025/6vms_21243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vms_21243/02_2025/6vms_21243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vms_21243/02_2025/6vms_21243.map" model { file = "/net/cci-nas-00/data/ceres_data/6vms_21243/02_2025/6vms_21243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vms_21243/02_2025/6vms_21243.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Br 1 7.06 5 S 65 5.16 5 C 5705 2.51 5 N 1512 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8953 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1823 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 454 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "E" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1782 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2244 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'08Y': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.38, per 1000 atoms: 0.60 Number of scatterers: 8953 At special positions: 0 Unit cell: (103.75, 117.86, 128.65, 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) Br 1 34.99 S 65 16.00 O 1670 8.00 N 1512 7.00 C 5705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS R 399 " - pdb=" SG CYS R 401 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 38.4% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.839A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.527A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.864A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.589A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.518A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.507A pdb=" N ALA C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.668A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'R' and resid 35 through 40 removed outlier: 3.515A pdb=" N LEU R 40 " --> pdb=" O TYR R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 62 removed outlier: 3.547A pdb=" N ILE R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU R 54 " --> pdb=" O PHE R 50 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N CYS R 56 " --> pdb=" O ASN R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 87 removed outlier: 3.555A pdb=" N TYR R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 97 Processing helix chain 'R' and resid 105 through 138 Processing helix chain 'R' and resid 144 through 168 removed outlier: 3.670A pdb=" N LYS R 149 " --> pdb=" O ARG R 145 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ARG R 150 " --> pdb=" O TYR R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 171 No H-bonds generated for 'chain 'R' and resid 169 through 171' Processing helix chain 'R' and resid 186 through 198 removed outlier: 3.675A pdb=" N VAL R 190 " --> pdb=" O ASN R 186 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL R 196 " --> pdb=" O TYR R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 224 removed outlier: 4.453A pdb=" N ASN R 224 " --> pdb=" O ARG R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 363 through 399 removed outlier: 3.526A pdb=" N LYS R 369 " --> pdb=" O GLN R 365 " (cutoff:3.500A) Proline residue: R 388 - end of helix removed outlier: 3.609A pdb=" N ILE R 397 " --> pdb=" O HIS R 393 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS R 398 " --> pdb=" O ILE R 394 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 426 removed outlier: 4.127A pdb=" N TYR R 408 " --> pdb=" O PRO R 404 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA R 410 " --> pdb=" O VAL R 406 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN R 418 " --> pdb=" O LEU R 414 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 430 through 441 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.737A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.527A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.985A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.924A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.804A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.773A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.366A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.943A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.624A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.176A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.822A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.822A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1269 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: 2.76 Time building geometry restraints manager: 2.65 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: 2875 1.34 - 1.47: 2292 1.47 - 1.60: 3880 1.60 - 1.73: 0 1.73 - 1.86: 94 Bond restraints: 9141 Sorted by residual: bond pdb=" C25 08Y R 601 " pdb=" C29 08Y R 601 " ideal model delta sigma weight residual 1.367 1.403 -0.036 2.00e-02 2.50e+03 3.17e+00 bond pdb=" C LEU R 407 " pdb=" N TYR R 408 " ideal model delta sigma weight residual 1.335 1.351 -0.017 1.25e-02 6.40e+03 1.84e+00 bond pdb=" C2 08Y R 601 " pdb=" O1 08Y R 601 " ideal model delta sigma weight residual 1.398 1.425 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" CB VAL A 342 " pdb=" CG2 VAL A 342 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.36e+00 bond pdb=" CG LEU B 336 " pdb=" CD2 LEU B 336 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.31e+00 ... (remaining 9136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 12050 1.82 - 3.64: 304 3.64 - 5.47: 41 5.47 - 7.29: 5 7.29 - 9.11: 1 Bond angle restraints: 12401 Sorted by residual: angle pdb=" CB LYS C 32 " pdb=" CG LYS C 32 " pdb=" CD LYS C 32 " ideal model delta sigma weight residual 111.30 120.41 -9.11 2.30e+00 1.89e-01 1.57e+01 angle pdb=" N MET E 192 " pdb=" CA MET E 192 " pdb=" C MET E 192 " ideal model delta sigma weight residual 110.80 117.44 -6.64 2.13e+00 2.20e-01 9.71e+00 angle pdb=" N ARG R 361 " pdb=" CA ARG R 361 " pdb=" C ARG R 361 " ideal model delta sigma weight residual 110.80 117.11 -6.31 2.13e+00 2.20e-01 8.77e+00 angle pdb=" N GLY E 33 " pdb=" CA GLY E 33 " pdb=" C GLY E 33 " ideal model delta sigma weight residual 112.89 108.41 4.48 1.58e+00 4.01e-01 8.05e+00 angle pdb=" C ILE B 338 " pdb=" N TRP B 339 " pdb=" CA TRP B 339 " ideal model delta sigma weight residual 123.05 126.75 -3.70 1.40e+00 5.10e-01 7.00e+00 ... (remaining 12396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5249 17.47 - 34.94: 195 34.94 - 52.41: 35 52.41 - 69.88: 18 69.88 - 87.35: 6 Dihedral angle restraints: 5503 sinusoidal: 2192 harmonic: 3311 Sorted by residual: dihedral pdb=" CB CYS R 399 " pdb=" SG CYS R 399 " pdb=" SG CYS R 401 " pdb=" CB CYS R 401 " ideal model delta sinusoidal sigma weight residual -86.00 -145.68 59.68 1 1.00e+01 1.00e-02 4.75e+01 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 93.00 149.27 -56.27 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CA PRO R 139 " pdb=" C PRO R 139 " pdb=" N MET R 140 " pdb=" CA MET R 140 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 5500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 765 0.029 - 0.058: 431 0.058 - 0.087: 140 0.087 - 0.116: 70 0.116 - 0.145: 13 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CA ILE A 221 " pdb=" N ILE A 221 " pdb=" C ILE A 221 " pdb=" CB ILE A 221 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA VAL B 135 " pdb=" N VAL B 135 " pdb=" C VAL B 135 " pdb=" CB VAL B 135 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1416 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 08Y R 601 " -0.099 2.00e-02 2.50e+03 8.71e-02 2.28e+02 pdb=" C23 08Y R 601 " 0.157 2.00e-02 2.50e+03 pdb=" C24 08Y R 601 " -0.063 2.00e-02 2.50e+03 pdb=" C25 08Y R 601 " -0.032 2.00e-02 2.50e+03 pdb=" C26 08Y R 601 " -0.107 2.00e-02 2.50e+03 pdb=" C28 08Y R 601 " -0.087 2.00e-02 2.50e+03 pdb=" C29 08Y R 601 " -0.021 2.00e-02 2.50e+03 pdb=" C30 08Y R 601 " 0.092 2.00e-02 2.50e+03 pdb=" C31 08Y R 601 " 0.023 2.00e-02 2.50e+03 pdb=" C32 08Y R 601 " 0.122 2.00e-02 2.50e+03 pdb=" N5 08Y R 601 " -0.056 2.00e-02 2.50e+03 pdb="BR 08Y R 601 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 08Y R 601 " 0.060 2.00e-02 2.50e+03 5.54e-02 4.61e+01 pdb=" C3 08Y R 601 " -0.071 2.00e-02 2.50e+03 pdb=" C6 08Y R 601 " -0.074 2.00e-02 2.50e+03 pdb=" C9 08Y R 601 " 0.008 2.00e-02 2.50e+03 pdb=" N2 08Y R 601 " 0.011 2.00e-02 2.50e+03 pdb=" O4 08Y R 601 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 08Y R 601 " -0.067 2.00e-02 2.50e+03 4.51e-02 3.05e+01 pdb=" C3 08Y R 601 " 0.035 2.00e-02 2.50e+03 pdb=" C5 08Y R 601 " 0.055 2.00e-02 2.50e+03 pdb=" C8 08Y R 601 " -0.000 2.00e-02 2.50e+03 pdb=" N1 08Y R 601 " 0.028 2.00e-02 2.50e+03 pdb=" O3 08Y R 601 " -0.051 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 112 2.65 - 3.21: 8326 3.21 - 3.77: 13346 3.77 - 4.34: 19193 4.34 - 4.90: 31065 Nonbonded interactions: 72042 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.082 3.040 nonbonded pdb=" O ALA A 41 " pdb=" OG SER A 44 " model vdw 2.103 3.040 nonbonded pdb=" O SER E 30 " pdb=" OG SER E 53 " model vdw 2.116 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.126 3.040 nonbonded pdb=" OG SER E 106 " pdb=" OH TYR E 190 " model vdw 2.227 3.040 ... (remaining 72037 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.870 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 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 : 0.005 0.039 9141 Z= 0.306 Angle : 0.704 9.108 12401 Z= 0.393 Chirality : 0.043 0.145 1419 Planarity : 0.005 0.087 1557 Dihedral : 11.035 87.351 3353 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.27 (0.24), residues: 1121 helix: -0.49 (0.24), residues: 380 sheet: 0.63 (0.29), residues: 275 loop : -0.23 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 82 HIS 0.005 0.001 HIS R 106 PHE 0.016 0.002 PHE B 234 TYR 0.012 0.002 TYR R 146 ARG 0.011 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.7739 (t80) cc_final: 0.7508 (t80) REVERT: A 228 SER cc_start: 0.7575 (p) cc_final: 0.6988 (p) REVERT: A 273 LEU cc_start: 0.8501 (mt) cc_final: 0.8101 (tt) REVERT: B 76 ASP cc_start: 0.6632 (t0) cc_final: 0.6373 (t0) REVERT: B 171 ILE cc_start: 0.7446 (tp) cc_final: 0.7173 (tp) REVERT: E 60 TYR cc_start: 0.7906 (m-80) cc_final: 0.7482 (m-80) REVERT: E 68 PHE cc_start: 0.7615 (m-10) cc_final: 0.7041 (m-10) REVERT: E 71 SER cc_start: 0.6618 (t) cc_final: 0.6020 (p) REVERT: E 83 MET cc_start: 0.8704 (mtt) cc_final: 0.8474 (mtm) REVERT: E 234 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7945 (mm-30) REVERT: R 164 PHE cc_start: 0.7718 (t80) cc_final: 0.7498 (t80) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.2702 time to fit residues: 109.3544 Evaluate side-chains 175 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 220 GLN B 266 HIS B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN C 44 HIS ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN R 106 HIS R 179 GLN ** R 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.170733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.142251 restraints weight = 12004.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142443 restraints weight = 13020.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.143283 restraints weight = 11894.644| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9141 Z= 0.263 Angle : 0.683 7.998 12401 Z= 0.369 Chirality : 0.047 0.208 1419 Planarity : 0.005 0.058 1557 Dihedral : 5.787 65.932 1312 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.27 % Allowed : 11.02 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1121 helix: 0.76 (0.26), residues: 394 sheet: 0.76 (0.29), residues: 279 loop : 0.14 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 100 HIS 0.013 0.002 HIS R 393 PHE 0.029 0.002 PHE R 390 TYR 0.021 0.002 TYR B 59 ARG 0.006 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.8364 (mt) cc_final: 0.7977 (tt) REVERT: A 345 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7887 (mttm) REVERT: B 59 TYR cc_start: 0.8544 (m-80) cc_final: 0.8217 (m-80) REVERT: B 76 ASP cc_start: 0.6670 (t0) cc_final: 0.6398 (t0) REVERT: B 188 MET cc_start: 0.8669 (mmm) cc_final: 0.8307 (mmm) REVERT: B 191 SER cc_start: 0.8233 (t) cc_final: 0.8013 (t) REVERT: B 266 HIS cc_start: 0.6493 (t-170) cc_final: 0.6139 (t70) REVERT: B 334 SER cc_start: 0.8309 (m) cc_final: 0.8073 (p) REVERT: R 91 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8238 (p) outliers start: 32 outliers final: 18 residues processed: 229 average time/residue: 0.2611 time to fit residues: 78.9103 Evaluate side-chains 186 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Chi-restraints excluded: chain R residue 433 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 0.0980 chunk 72 optimal weight: 6.9990 chunk 37 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 0.0870 chunk 61 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 220 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** R 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.167387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136105 restraints weight = 12319.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137295 restraints weight = 10747.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139320 restraints weight = 8875.996| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9141 Z= 0.167 Angle : 0.591 7.881 12401 Z= 0.316 Chirality : 0.044 0.147 1419 Planarity : 0.004 0.040 1557 Dihedral : 5.497 62.924 1312 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.04 % Allowed : 13.98 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.83 (0.25), residues: 1121 helix: 1.16 (0.27), residues: 392 sheet: 0.81 (0.29), residues: 275 loop : -0.03 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 100 HIS 0.007 0.001 HIS R 393 PHE 0.020 0.002 PHE R 172 TYR 0.018 0.001 TYR A 287 ARG 0.005 0.001 ARG R 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.8268 (mt) cc_final: 0.7920 (tt) REVERT: B 76 ASP cc_start: 0.6421 (t0) cc_final: 0.6162 (t0) REVERT: B 290 ASP cc_start: 0.8580 (m-30) cc_final: 0.8371 (m-30) REVERT: B 334 SER cc_start: 0.8307 (m) cc_final: 0.8085 (p) REVERT: C 28 ILE cc_start: 0.7282 (pt) cc_final: 0.7045 (pt) REVERT: E 192 MET cc_start: 0.8500 (ptt) cc_final: 0.7805 (ptt) REVERT: R 220 ARG cc_start: 0.5923 (ttt-90) cc_final: 0.5423 (ttt90) REVERT: R 413 TRP cc_start: 0.7329 (m100) cc_final: 0.6110 (m-10) outliers start: 20 outliers final: 16 residues processed: 200 average time/residue: 0.2450 time to fit residues: 65.5679 Evaluate side-chains 175 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Chi-restraints excluded: chain R residue 433 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 0.1980 chunk 95 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 108 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.163861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131996 restraints weight = 12195.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133193 restraints weight = 11585.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.134520 restraints weight = 8948.026| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9141 Z= 0.171 Angle : 0.574 6.635 12401 Z= 0.303 Chirality : 0.044 0.185 1419 Planarity : 0.003 0.035 1557 Dihedral : 5.252 59.401 1312 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.65 % Allowed : 15.10 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1121 helix: 1.30 (0.28), residues: 389 sheet: 0.57 (0.28), residues: 286 loop : -0.10 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 100 HIS 0.003 0.001 HIS A 244 PHE 0.016 0.001 PHE R 172 TYR 0.014 0.001 TYR B 59 ARG 0.007 0.001 ARG R 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.8185 (mt) cc_final: 0.7907 (tt) REVERT: B 76 ASP cc_start: 0.6452 (t0) cc_final: 0.6174 (t0) REVERT: B 175 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7313 (mm110) REVERT: B 334 SER cc_start: 0.8373 (m) cc_final: 0.8152 (p) REVERT: E 192 MET cc_start: 0.8639 (ptt) cc_final: 0.8119 (ptt) REVERT: R 148 SER cc_start: 0.8638 (m) cc_final: 0.8136 (t) REVERT: R 393 HIS cc_start: 0.8008 (t-90) cc_final: 0.7796 (t-170) outliers start: 26 outliers final: 16 residues processed: 200 average time/residue: 0.2452 time to fit residues: 65.1935 Evaluate side-chains 181 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Chi-restraints excluded: chain R residue 433 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.164201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134700 restraints weight = 12102.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.135803 restraints weight = 12853.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136378 restraints weight = 10356.449| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9141 Z= 0.192 Angle : 0.563 7.120 12401 Z= 0.301 Chirality : 0.044 0.226 1419 Planarity : 0.004 0.037 1557 Dihedral : 5.123 57.753 1312 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.76 % Allowed : 16.22 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1121 helix: 1.63 (0.28), residues: 380 sheet: 0.42 (0.28), residues: 291 loop : -0.17 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 111 HIS 0.002 0.001 HIS R 393 PHE 0.025 0.002 PHE R 389 TYR 0.018 0.001 TYR E 190 ARG 0.014 0.001 ARG R 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7625 (m-30) cc_final: 0.7290 (m-30) REVERT: A 33 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7439 (mt-10) REVERT: A 273 LEU cc_start: 0.8231 (mt) cc_final: 0.8014 (tt) REVERT: B 76 ASP cc_start: 0.6684 (t0) cc_final: 0.6373 (t0) REVERT: B 175 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7523 (mm110) REVERT: B 191 SER cc_start: 0.8390 (t) cc_final: 0.7644 (t) REVERT: B 234 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8083 (m-80) REVERT: E 18 ARG cc_start: 0.7622 (tpp-160) cc_final: 0.7420 (tpp-160) REVERT: E 93 MET cc_start: 0.8673 (tpp) cc_final: 0.8026 (ttt) REVERT: E 192 MET cc_start: 0.8550 (ptt) cc_final: 0.7963 (ptt) REVERT: R 108 ASP cc_start: 0.6452 (m-30) cc_final: 0.6077 (m-30) REVERT: R 148 SER cc_start: 0.8807 (m) cc_final: 0.8142 (t) REVERT: R 369 LYS cc_start: 0.5919 (mmmt) cc_final: 0.5549 (tptt) outliers start: 27 outliers final: 19 residues processed: 203 average time/residue: 0.2377 time to fit residues: 64.6524 Evaluate side-chains 186 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Chi-restraints excluded: chain R residue 433 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 chunk 66 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.161001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129119 restraints weight = 12237.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130336 restraints weight = 11975.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.132301 restraints weight = 9464.292| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9141 Z= 0.164 Angle : 0.576 10.054 12401 Z= 0.300 Chirality : 0.044 0.175 1419 Planarity : 0.003 0.034 1557 Dihedral : 5.089 57.832 1312 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.45 % Allowed : 18.06 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1121 helix: 1.50 (0.28), residues: 384 sheet: 0.43 (0.28), residues: 291 loop : -0.24 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 100 HIS 0.003 0.001 HIS A 188 PHE 0.015 0.001 PHE R 102 TYR 0.016 0.001 TYR E 190 ARG 0.007 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7530 (m-30) cc_final: 0.7239 (m-30) REVERT: A 33 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7425 (mt-10) REVERT: A 273 LEU cc_start: 0.8174 (mt) cc_final: 0.7948 (tt) REVERT: B 76 ASP cc_start: 0.6563 (t0) cc_final: 0.6218 (t0) REVERT: B 191 SER cc_start: 0.8355 (t) cc_final: 0.7600 (t) REVERT: B 234 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: E 34 MET cc_start: 0.8120 (mmm) cc_final: 0.7883 (mmt) REVERT: E 93 MET cc_start: 0.8675 (tpp) cc_final: 0.8049 (ttt) REVERT: E 192 MET cc_start: 0.8458 (ptt) cc_final: 0.7844 (ptt) REVERT: R 108 ASP cc_start: 0.6637 (m-30) cc_final: 0.6331 (m-30) REVERT: R 140 MET cc_start: 0.7659 (mmm) cc_final: 0.7186 (mmm) REVERT: R 369 LYS cc_start: 0.5876 (mmmt) cc_final: 0.5440 (tptt) outliers start: 24 outliers final: 18 residues processed: 186 average time/residue: 0.2524 time to fit residues: 62.0882 Evaluate side-chains 188 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Chi-restraints excluded: chain R residue 433 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122030 restraints weight = 12280.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122080 restraints weight = 11302.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.124035 restraints weight = 10652.132| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9141 Z= 0.209 Angle : 0.572 8.951 12401 Z= 0.303 Chirality : 0.044 0.248 1419 Planarity : 0.004 0.048 1557 Dihedral : 5.077 56.378 1312 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.27 % Allowed : 18.88 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.71 (0.25), residues: 1121 helix: 1.54 (0.27), residues: 385 sheet: 0.41 (0.29), residues: 286 loop : -0.33 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 100 HIS 0.003 0.001 HIS B 142 PHE 0.017 0.002 PHE R 102 TYR 0.020 0.001 TYR E 190 ARG 0.012 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7761 (m-30) cc_final: 0.7471 (m-30) REVERT: A 33 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7547 (mt-10) REVERT: A 287 TYR cc_start: 0.7574 (m-80) cc_final: 0.7261 (m-80) REVERT: B 76 ASP cc_start: 0.6707 (t0) cc_final: 0.6393 (t0) REVERT: B 191 SER cc_start: 0.8648 (t) cc_final: 0.8002 (t) REVERT: B 234 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8395 (m-80) REVERT: C 15 LEU cc_start: 0.7373 (mp) cc_final: 0.7033 (tp) REVERT: C 58 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6333 (tt0) REVERT: E 93 MET cc_start: 0.8637 (tpp) cc_final: 0.8159 (ttt) REVERT: E 192 MET cc_start: 0.8430 (ptt) cc_final: 0.7715 (ptt) REVERT: R 108 ASP cc_start: 0.6889 (m-30) cc_final: 0.6640 (m-30) REVERT: R 140 MET cc_start: 0.7767 (mmm) cc_final: 0.7253 (mmm) REVERT: R 369 LYS cc_start: 0.6106 (mmmt) cc_final: 0.5672 (tptt) REVERT: R 403 ILE cc_start: 0.8093 (tp) cc_final: 0.7570 (mm) outliers start: 32 outliers final: 20 residues processed: 203 average time/residue: 0.2412 time to fit residues: 64.8418 Evaluate side-chains 192 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.156775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124811 restraints weight = 12451.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.124849 restraints weight = 11483.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.126891 restraints weight = 10787.489| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.6428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9141 Z= 0.177 Angle : 0.578 9.784 12401 Z= 0.307 Chirality : 0.044 0.269 1419 Planarity : 0.004 0.042 1557 Dihedral : 5.001 54.697 1312 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.76 % Allowed : 20.00 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1121 helix: 1.35 (0.27), residues: 386 sheet: 0.47 (0.29), residues: 281 loop : -0.49 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 100 HIS 0.003 0.001 HIS A 188 PHE 0.024 0.001 PHE R 390 TYR 0.017 0.001 TYR E 190 ARG 0.011 0.001 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7561 (m-30) cc_final: 0.7354 (m-30) REVERT: A 33 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7512 (mt-10) REVERT: B 76 ASP cc_start: 0.6495 (t0) cc_final: 0.6207 (t0) REVERT: B 191 SER cc_start: 0.8605 (t) cc_final: 0.7976 (t) REVERT: B 234 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: C 11 GLN cc_start: 0.5477 (mp10) cc_final: 0.4602 (mt0) REVERT: C 15 LEU cc_start: 0.7304 (mp) cc_final: 0.7083 (tt) REVERT: E 34 MET cc_start: 0.8207 (mmm) cc_final: 0.7905 (mmt) REVERT: E 93 MET cc_start: 0.8599 (tpp) cc_final: 0.8124 (ttt) REVERT: E 192 MET cc_start: 0.8485 (ptt) cc_final: 0.7773 (ptt) REVERT: R 140 MET cc_start: 0.7670 (mmm) cc_final: 0.7211 (mmm) REVERT: R 369 LYS cc_start: 0.5937 (mmmt) cc_final: 0.5582 (tptt) REVERT: R 403 ILE cc_start: 0.8048 (tp) cc_final: 0.7531 (mm) outliers start: 27 outliers final: 19 residues processed: 200 average time/residue: 0.2499 time to fit residues: 66.5436 Evaluate side-chains 190 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 0.0050 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 49 optimal weight: 0.0170 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 overall best weight: 0.4832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.157641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.125736 restraints weight = 12248.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125893 restraints weight = 12154.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.128300 restraints weight = 10398.486| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.6636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9141 Z= 0.166 Angle : 0.582 11.617 12401 Z= 0.306 Chirality : 0.044 0.225 1419 Planarity : 0.004 0.078 1557 Dihedral : 4.913 52.798 1312 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.14 % Allowed : 21.02 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1121 helix: 1.25 (0.27), residues: 396 sheet: 0.52 (0.30), residues: 276 loop : -0.47 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.002 0.001 HIS A 188 PHE 0.023 0.001 PHE R 390 TYR 0.021 0.001 TYR A 287 ARG 0.014 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7486 (mt-10) REVERT: B 76 ASP cc_start: 0.6495 (t0) cc_final: 0.6147 (t0) REVERT: B 147 SER cc_start: 0.8839 (p) cc_final: 0.8544 (t) REVERT: B 215 GLU cc_start: 0.7062 (tp30) cc_final: 0.6618 (tp30) REVERT: C 11 GLN cc_start: 0.5485 (mp10) cc_final: 0.4584 (mt0) REVERT: E 34 MET cc_start: 0.8198 (mmm) cc_final: 0.7929 (mmt) REVERT: E 192 MET cc_start: 0.8481 (ptt) cc_final: 0.7679 (ptt) REVERT: R 140 MET cc_start: 0.7644 (mmm) cc_final: 0.7219 (mmm) REVERT: R 369 LYS cc_start: 0.5770 (mmmt) cc_final: 0.5456 (tptt) REVERT: R 403 ILE cc_start: 0.8062 (tp) cc_final: 0.7539 (mm) outliers start: 21 outliers final: 18 residues processed: 190 average time/residue: 0.2482 time to fit residues: 62.3752 Evaluate side-chains 186 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 44 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.152093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119328 restraints weight = 12292.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119085 restraints weight = 11954.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121200 restraints weight = 11138.711| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.6974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9141 Z= 0.272 Angle : 0.649 12.336 12401 Z= 0.336 Chirality : 0.046 0.204 1419 Planarity : 0.004 0.044 1557 Dihedral : 5.074 53.452 1312 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.04 % Allowed : 21.43 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1121 helix: 1.26 (0.27), residues: 392 sheet: 0.36 (0.30), residues: 289 loop : -0.54 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.032 0.002 PHE R 390 TYR 0.023 0.001 TYR E 190 ARG 0.015 0.001 ARG C 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: A 228 SER cc_start: 0.7820 (p) cc_final: 0.7461 (t) REVERT: A 232 LEU cc_start: 0.8070 (mt) cc_final: 0.7818 (mt) REVERT: B 76 ASP cc_start: 0.6830 (t0) cc_final: 0.6543 (t0) REVERT: B 191 SER cc_start: 0.8818 (t) cc_final: 0.8507 (t) REVERT: C 11 GLN cc_start: 0.5430 (mp10) cc_final: 0.4607 (mt0) REVERT: E 192 MET cc_start: 0.8509 (ptt) cc_final: 0.7647 (ptt) REVERT: R 140 MET cc_start: 0.7774 (mmm) cc_final: 0.7325 (mmm) REVERT: R 369 LYS cc_start: 0.5991 (mmmt) cc_final: 0.5610 (tptt) REVERT: R 403 ILE cc_start: 0.8106 (tp) cc_final: 0.7576 (mm) outliers start: 20 outliers final: 19 residues processed: 200 average time/residue: 0.2600 time to fit residues: 68.2299 Evaluate side-chains 187 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 83 optimal weight: 0.0070 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.153747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121811 restraints weight = 12338.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121069 restraints weight = 11287.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.123307 restraints weight = 10894.956| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.7190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9141 Z= 0.199 Angle : 0.619 12.719 12401 Z= 0.322 Chirality : 0.045 0.211 1419 Planarity : 0.004 0.043 1557 Dihedral : 5.040 55.536 1312 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.45 % Allowed : 21.73 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.46 (0.25), residues: 1121 helix: 1.34 (0.27), residues: 386 sheet: 0.33 (0.29), residues: 288 loop : -0.54 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.003 0.001 HIS R 393 PHE 0.027 0.001 PHE R 390 TYR 0.024 0.001 TYR A 287 ARG 0.013 0.001 ARG C 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2851.80 seconds wall clock time: 52 minutes 4.12 seconds (3124.12 seconds total)