Starting phenix.real_space_refine on Tue Sep 24 22:27:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/09_2024/6vms_21243.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/09_2024/6vms_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/09_2024/6vms_21243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/09_2024/6vms_21243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/09_2024/6vms_21243.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/09_2024/6vms_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-5461/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: 5.64, per 1000 atoms: 0.63 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 953.7 milliseconds 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: 1.21 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: 2.66 Time building geometry restraints manager: 2.69 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: 1.900 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.040 Find NCS groups from input model: 0.090 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.590 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 0.980 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: 0.2654 time to fit residues: 107.0007 Evaluate side-chains 175 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 fitting. rotamer outliers: 32 poor density : 210 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.8559 (mt) cc_final: 0.8101 (tt) REVERT: A 345 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7759 (mttm) REVERT: B 59 TYR cc_start: 0.8689 (m-80) cc_final: 0.8386 (m-80) REVERT: B 76 ASP cc_start: 0.6886 (t0) cc_final: 0.6616 (t0) REVERT: B 188 MET cc_start: 0.8638 (mmm) cc_final: 0.8195 (mmm) REVERT: B 191 SER cc_start: 0.8228 (t) cc_final: 0.7965 (t) REVERT: B 266 HIS cc_start: 0.6666 (t-170) cc_final: 0.6217 (t70) REVERT: E 14 PRO cc_start: 0.7262 (Cg_endo) cc_final: 0.7057 (Cg_exo) REVERT: E 18 ARG cc_start: 0.7613 (tpp-160) cc_final: 0.7328 (tpp-160) REVERT: E 60 TYR cc_start: 0.7973 (m-80) cc_final: 0.7496 (m-80) REVERT: E 71 SER cc_start: 0.6665 (t) cc_final: 0.6424 (p) REVERT: E 197 SER cc_start: 0.9228 (m) cc_final: 0.8883 (p) REVERT: E 223 ASP cc_start: 0.6681 (m-30) cc_final: 0.6477 (m-30) REVERT: E 234 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7877 (mm-30) REVERT: R 91 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8220 (p) outliers start: 32 outliers final: 18 residues processed: 229 average time/residue: 0.2485 time to fit residues: 74.7896 Evaluate side-chains 188 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 55 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4567 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= 0.206 Angle : 0.604 7.860 12401 Z= 0.323 Chirality : 0.044 0.155 1419 Planarity : 0.004 0.039 1557 Dihedral : 5.506 62.264 1312 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.45 % Allowed : 14.29 % Favored : 83.27 % 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: 0.81 (0.25), residues: 1121 helix: 1.23 (0.27), residues: 386 sheet: 0.63 (0.29), residues: 284 loop : 0.00 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 100 HIS 0.009 0.001 HIS R 393 PHE 0.018 0.002 PHE R 172 TYR 0.018 0.001 TYR A 287 ARG 0.004 0.001 ARG A 242 *********************** 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 222 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 198 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.8552 (mt) cc_final: 0.8119 (tt) REVERT: A 313 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7389 (mtm-85) REVERT: B 10 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6928 (pt0) REVERT: B 76 ASP cc_start: 0.6984 (t0) cc_final: 0.6727 (t0) REVERT: B 175 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7396 (mm110) REVERT: C 28 ILE cc_start: 0.7355 (pt) cc_final: 0.7126 (pt) REVERT: E 14 PRO cc_start: 0.6901 (Cg_endo) cc_final: 0.6643 (Cg_exo) REVERT: E 18 ARG cc_start: 0.7714 (tpp-160) cc_final: 0.7280 (tpp-160) REVERT: E 60 TYR cc_start: 0.8069 (m-80) cc_final: 0.7552 (m-80) REVERT: E 71 SER cc_start: 0.6573 (t) cc_final: 0.6350 (p) REVERT: E 76 LYS cc_start: 0.8049 (mtpt) cc_final: 0.7760 (mptt) REVERT: E 83 MET cc_start: 0.8647 (mtm) cc_final: 0.8426 (mtm) REVERT: E 139 VAL cc_start: 0.8571 (t) cc_final: 0.8275 (m) REVERT: E 192 MET cc_start: 0.7762 (ptt) cc_final: 0.7487 (ptt) REVERT: E 197 SER cc_start: 0.9243 (m) cc_final: 0.8873 (p) REVERT: E 234 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7889 (mm-30) REVERT: R 93 TYR cc_start: 0.7247 (t80) cc_final: 0.6943 (t80) REVERT: R 220 ARG cc_start: 0.6108 (ttt-90) cc_final: 0.5610 (ttt90) outliers start: 24 outliers final: 17 residues processed: 212 average time/residue: 0.2280 time to fit residues: 64.7723 Evaluate side-chains 194 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 176 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 313 ARG Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 334 SER 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 98 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9141 Z= 0.237 Angle : 0.600 6.597 12401 Z= 0.318 Chirality : 0.045 0.199 1419 Planarity : 0.004 0.040 1557 Dihedral : 5.346 58.896 1312 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.57 % Allowed : 15.20 % Favored : 81.22 % 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: 0.67 (0.25), residues: 1121 helix: 1.26 (0.28), residues: 386 sheet: 0.47 (0.29), residues: 284 loop : -0.17 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 100 HIS 0.006 0.001 HIS A 244 PHE 0.024 0.002 PHE R 172 TYR 0.017 0.001 TYR E 190 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 229 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 194 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8283 (m-30) cc_final: 0.7972 (m-30) REVERT: A 33 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 240 MET cc_start: 0.6585 (tpt) cc_final: 0.5977 (ppp) REVERT: A 248 LYS cc_start: 0.8817 (mttt) cc_final: 0.8551 (tttm) REVERT: A 273 LEU cc_start: 0.8584 (mt) cc_final: 0.8227 (tt) REVERT: A 313 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7371 (mtm-85) REVERT: B 76 ASP cc_start: 0.6933 (t0) cc_final: 0.6653 (t0) REVERT: B 88 ASN cc_start: 0.8458 (m-40) cc_final: 0.8171 (m110) REVERT: B 175 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7556 (mm110) REVERT: B 234 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8466 (m-80) REVERT: C 13 ARG cc_start: 0.7430 (mtm-85) cc_final: 0.7194 (mtm-85) REVERT: E 18 ARG cc_start: 0.7683 (tpp-160) cc_final: 0.7142 (tpp-160) REVERT: E 60 TYR cc_start: 0.7989 (m-80) cc_final: 0.7532 (m-80) REVERT: E 71 SER cc_start: 0.6733 (t) cc_final: 0.6477 (p) REVERT: E 192 MET cc_start: 0.7733 (ptt) cc_final: 0.7221 (ptt) REVERT: E 197 SER cc_start: 0.9263 (m) cc_final: 0.8901 (p) REVERT: R 93 TYR cc_start: 0.7196 (t80) cc_final: 0.6927 (t80) REVERT: R 108 ASP cc_start: 0.6747 (m-30) cc_final: 0.6394 (m-30) REVERT: R 148 SER cc_start: 0.8714 (m) cc_final: 0.8160 (t) REVERT: R 220 ARG cc_start: 0.6206 (ttt-90) cc_final: 0.5939 (tpt-90) REVERT: R 403 ILE cc_start: 0.8235 (tp) cc_final: 0.7674 (mm) outliers start: 35 outliers final: 22 residues processed: 216 average time/residue: 0.2361 time to fit residues: 68.7738 Evaluate side-chains 195 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 313 ARG 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 187 LEU 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 78 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 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 88 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 91 HIS B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.6871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 9141 Z= 0.481 Angle : 0.776 9.851 12401 Z= 0.410 Chirality : 0.051 0.228 1419 Planarity : 0.005 0.039 1557 Dihedral : 5.874 58.786 1312 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.20 % Allowed : 15.31 % Favored : 79.49 % 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: -0.04 (0.25), residues: 1121 helix: 0.75 (0.27), residues: 386 sheet: -0.11 (0.28), residues: 299 loop : -0.52 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 211 HIS 0.012 0.002 HIS E 232 PHE 0.034 0.003 PHE R 390 TYR 0.043 0.002 TYR E 190 ARG 0.007 0.001 ARG R 217 *********************** 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 247 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 196 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8413 (m-30) cc_final: 0.8105 (m-30) REVERT: A 10 LYS cc_start: 0.8372 (mttt) cc_final: 0.8143 (mtpt) REVERT: A 228 SER cc_start: 0.7878 (OUTLIER) cc_final: 0.7506 (t) REVERT: A 248 LYS cc_start: 0.8961 (mttt) cc_final: 0.8674 (tmtt) REVERT: A 273 LEU cc_start: 0.8764 (mt) cc_final: 0.8412 (tt) REVERT: A 313 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7471 (mtm-85) REVERT: B 76 ASP cc_start: 0.7624 (t0) cc_final: 0.7408 (t0) REVERT: B 175 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7674 (mm110) REVERT: B 200 VAL cc_start: 0.9627 (p) cc_final: 0.9394 (m) REVERT: B 228 ASP cc_start: 0.8031 (m-30) cc_final: 0.7673 (m-30) REVERT: C 15 LEU cc_start: 0.7781 (mp) cc_final: 0.7355 (tp) REVERT: E 73 ASP cc_start: 0.7137 (t0) cc_final: 0.6818 (t0) REVERT: E 197 SER cc_start: 0.9233 (m) cc_final: 0.8935 (p) REVERT: E 234 GLU cc_start: 0.8353 (pt0) cc_final: 0.8082 (pt0) REVERT: R 220 ARG cc_start: 0.6275 (ttt-90) cc_final: 0.5966 (tpt-90) REVERT: R 369 LYS cc_start: 0.6706 (mmmt) cc_final: 0.6205 (tptt) REVERT: R 377 ILE cc_start: 0.8496 (mm) cc_final: 0.8234 (mt) REVERT: R 433 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.6898 (t80) outliers start: 51 outliers final: 37 residues processed: 225 average time/residue: 0.2312 time to fit residues: 69.2925 Evaluate side-chains 205 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 206 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 344 ILE 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 249 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 SER 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 118 THR Chi-restraints excluded: chain E residue 138 ILE 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 78 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 183 ILE Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 200 VAL 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 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.7017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9141 Z= 0.226 Angle : 0.605 9.319 12401 Z= 0.321 Chirality : 0.045 0.222 1419 Planarity : 0.004 0.036 1557 Dihedral : 5.501 60.535 1312 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.67 % Allowed : 18.88 % Favored : 77.45 % 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: 0.19 (0.25), residues: 1121 helix: 1.11 (0.27), residues: 383 sheet: -0.00 (0.28), residues: 291 loop : -0.54 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 100 HIS 0.003 0.001 HIS R 393 PHE 0.030 0.002 PHE R 390 TYR 0.029 0.001 TYR E 190 ARG 0.008 0.001 ARG R 217 *********************** 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 221 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 185 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8332 (m-30) cc_final: 0.8010 (m-30) REVERT: A 33 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7759 (mt-10) REVERT: A 187 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7814 (p) REVERT: A 228 SER cc_start: 0.7906 (OUTLIER) cc_final: 0.7495 (t) REVERT: A 248 LYS cc_start: 0.8999 (mttt) cc_final: 0.8690 (tmtt) REVERT: A 273 LEU cc_start: 0.8718 (mt) cc_final: 0.8427 (tt) REVERT: A 313 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7427 (mtm-85) REVERT: B 76 ASP cc_start: 0.7427 (t0) cc_final: 0.7165 (t0) REVERT: B 254 ASP cc_start: 0.8152 (t0) cc_final: 0.7892 (m-30) REVERT: C 15 LEU cc_start: 0.7735 (mp) cc_final: 0.7399 (tp) REVERT: C 32 LYS cc_start: 0.7882 (ptmm) cc_final: 0.7361 (ttpp) REVERT: E 18 ARG cc_start: 0.7733 (tpp-160) cc_final: 0.7416 (tpp-160) REVERT: E 73 ASP cc_start: 0.7171 (t0) cc_final: 0.6813 (t0) REVERT: E 192 MET cc_start: 0.7705 (ptt) cc_final: 0.7482 (ptt) REVERT: E 197 SER cc_start: 0.9283 (m) cc_final: 0.8914 (p) REVERT: E 234 GLU cc_start: 0.8424 (pt0) cc_final: 0.8129 (pt0) REVERT: R 369 LYS cc_start: 0.6420 (mmmt) cc_final: 0.5992 (tptt) outliers start: 36 outliers final: 25 residues processed: 207 average time/residue: 0.2355 time to fit residues: 65.0953 Evaluate side-chains 200 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 313 ARG 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 308 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 138 ILE 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 96 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN R 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.7247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9141 Z= 0.276 Angle : 0.594 7.916 12401 Z= 0.318 Chirality : 0.045 0.203 1419 Planarity : 0.004 0.036 1557 Dihedral : 5.388 56.530 1312 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.57 % Allowed : 19.80 % Favored : 76.63 % 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: 0.12 (0.25), residues: 1121 helix: 1.08 (0.27), residues: 386 sheet: -0.10 (0.28), residues: 287 loop : -0.57 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 100 HIS 0.003 0.001 HIS B 91 PHE 0.029 0.002 PHE R 390 TYR 0.030 0.002 TYR E 190 ARG 0.009 0.001 ARG C 13 *********************** 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 fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8244 (m-30) cc_final: 0.7933 (m-30) REVERT: A 33 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7734 (mt-10) REVERT: A 187 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7846 (p) REVERT: A 228 SER cc_start: 0.7913 (OUTLIER) cc_final: 0.7508 (t) REVERT: A 248 LYS cc_start: 0.9025 (mttt) cc_final: 0.8720 (tmtt) REVERT: A 313 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7449 (mtm-85) REVERT: B 76 ASP cc_start: 0.7484 (t0) cc_final: 0.7220 (t0) REVERT: B 130 GLU cc_start: 0.7749 (mp0) cc_final: 0.7420 (mp0) REVERT: C 15 LEU cc_start: 0.7805 (mp) cc_final: 0.7562 (tp) REVERT: C 32 LYS cc_start: 0.7808 (ptmm) cc_final: 0.7514 (ttpp) REVERT: E 192 MET cc_start: 0.7752 (ptt) cc_final: 0.7242 (ptt) REVERT: E 197 SER cc_start: 0.9285 (m) cc_final: 0.8917 (p) REVERT: E 234 GLU cc_start: 0.8487 (pt0) cc_final: 0.8194 (pt0) REVERT: R 220 ARG cc_start: 0.6416 (ttt-90) cc_final: 0.6215 (tpt-90) REVERT: R 369 LYS cc_start: 0.6378 (mmmt) cc_final: 0.5971 (tptt) outliers start: 35 outliers final: 27 residues processed: 195 average time/residue: 0.2437 time to fit residues: 62.9605 Evaluate side-chains 199 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 206 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 313 ARG 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 334 SER Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 138 ILE 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 E residue 246 GLU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 171 LEU 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 63 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.7411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9141 Z= 0.230 Angle : 0.594 8.571 12401 Z= 0.317 Chirality : 0.045 0.207 1419 Planarity : 0.004 0.036 1557 Dihedral : 5.339 56.349 1312 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.57 % Allowed : 19.90 % Favored : 76.53 % 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: 0.11 (0.25), residues: 1121 helix: 1.12 (0.27), residues: 386 sheet: -0.11 (0.29), residues: 279 loop : -0.63 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 100 HIS 0.007 0.001 HIS B 266 PHE 0.033 0.002 PHE R 390 TYR 0.028 0.001 TYR E 190 ARG 0.008 0.001 ARG A 32 *********************** 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 215 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 180 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8238 (m-30) cc_final: 0.7952 (m-30) REVERT: A 33 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7741 (mt-10) REVERT: A 228 SER cc_start: 0.7852 (OUTLIER) cc_final: 0.7370 (t) REVERT: A 248 LYS cc_start: 0.9051 (mttt) cc_final: 0.8692 (tmtt) REVERT: A 273 LEU cc_start: 0.8771 (mp) cc_final: 0.8347 (tt) REVERT: A 313 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7430 (mtm-85) REVERT: B 76 ASP cc_start: 0.7402 (t0) cc_final: 0.7135 (t0) REVERT: B 254 ASP cc_start: 0.8213 (t0) cc_final: 0.7987 (m-30) REVERT: C 15 LEU cc_start: 0.7811 (mp) cc_final: 0.7595 (tp) REVERT: C 32 LYS cc_start: 0.7935 (ptmm) cc_final: 0.7526 (ttpp) REVERT: E 18 ARG cc_start: 0.7598 (tpp-160) cc_final: 0.7293 (tpp-160) REVERT: E 73 ASP cc_start: 0.7201 (t0) cc_final: 0.6934 (t0) REVERT: E 192 MET cc_start: 0.7768 (ptt) cc_final: 0.6964 (ptt) REVERT: E 197 SER cc_start: 0.9285 (m) cc_final: 0.8907 (p) REVERT: E 234 GLU cc_start: 0.8505 (pt0) cc_final: 0.8214 (pt0) REVERT: R 217 ARG cc_start: 0.7045 (mmp-170) cc_final: 0.6785 (ttp-170) REVERT: R 369 LYS cc_start: 0.6318 (mmmt) cc_final: 0.5969 (tptt) outliers start: 35 outliers final: 28 residues processed: 197 average time/residue: 0.2478 time to fit residues: 64.7373 Evaluate side-chains 198 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 168 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 313 ARG 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 334 SER Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 186 GLN 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 E residue 246 GLU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 208 VAL 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 98 optimal weight: 0.3980 chunk 101 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 398 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9141 Z= 0.182 Angle : 0.584 11.403 12401 Z= 0.310 Chirality : 0.044 0.213 1419 Planarity : 0.004 0.035 1557 Dihedral : 5.239 55.943 1312 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.06 % Allowed : 20.92 % Favored : 76.02 % 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: 0.23 (0.25), residues: 1121 helix: 1.24 (0.27), residues: 387 sheet: 0.05 (0.29), residues: 279 loop : -0.63 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS R 393 PHE 0.030 0.001 PHE R 390 TYR 0.023 0.001 TYR C 40 ARG 0.008 0.000 ARG A 32 *********************** 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 213 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 0.842 Fit side-chains REVERT: A 33 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7746 (mt-10) REVERT: A 228 SER cc_start: 0.7810 (OUTLIER) cc_final: 0.7358 (t) REVERT: A 248 LYS cc_start: 0.9049 (mttt) cc_final: 0.8648 (tmtt) REVERT: A 313 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7454 (mtm-85) REVERT: B 33 ILE cc_start: 0.6470 (mp) cc_final: 0.6107 (mt) REVERT: B 67 SER cc_start: 0.9400 (m) cc_final: 0.8602 (t) REVERT: B 76 ASP cc_start: 0.7363 (t0) cc_final: 0.7077 (t0) REVERT: B 130 GLU cc_start: 0.7710 (mp0) cc_final: 0.7345 (mp0) REVERT: B 254 ASP cc_start: 0.8127 (t0) cc_final: 0.7899 (m-30) REVERT: B 290 ASP cc_start: 0.8669 (m-30) cc_final: 0.8358 (m-30) REVERT: C 32 LYS cc_start: 0.8018 (ptmm) cc_final: 0.7602 (ttpp) REVERT: E 18 ARG cc_start: 0.7548 (tpp-160) cc_final: 0.7323 (tpp-160) REVERT: E 39 GLN cc_start: 0.8250 (tp40) cc_final: 0.7891 (tp40) REVERT: E 73 ASP cc_start: 0.7333 (t0) cc_final: 0.7084 (t0) REVERT: E 83 MET cc_start: 0.8317 (mtm) cc_final: 0.7885 (mtm) REVERT: E 192 MET cc_start: 0.7699 (ptt) cc_final: 0.7262 (ptt) REVERT: E 197 SER cc_start: 0.9281 (m) cc_final: 0.8901 (p) REVERT: E 234 GLU cc_start: 0.8549 (pt0) cc_final: 0.8323 (pt0) REVERT: R 140 MET cc_start: 0.7990 (mmm) cc_final: 0.7435 (mmm) REVERT: R 218 ARG cc_start: 0.7028 (mtp85) cc_final: 0.6770 (mtt-85) REVERT: R 369 LYS cc_start: 0.6139 (mmmt) cc_final: 0.5813 (tptt) outliers start: 30 outliers final: 24 residues processed: 200 average time/residue: 0.2409 time to fit residues: 63.6116 Evaluate side-chains 198 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 150 THR 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 78 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 208 VAL 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 49 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.7644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9141 Z= 0.217 Angle : 0.609 12.455 12401 Z= 0.325 Chirality : 0.045 0.217 1419 Planarity : 0.004 0.068 1557 Dihedral : 5.213 55.289 1312 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.96 % Allowed : 21.63 % Favored : 75.41 % 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: 0.21 (0.25), residues: 1121 helix: 1.27 (0.27), residues: 388 sheet: -0.08 (0.30), residues: 278 loop : -0.61 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 100 HIS 0.004 0.001 HIS R 393 PHE 0.032 0.002 PHE R 390 TYR 0.026 0.001 TYR C 40 ARG 0.009 0.001 ARG R 220 ********************** 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 204 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 175 time to evaluate : 1.028 Fit side-chains REVERT: A 33 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7757 (mt-10) REVERT: A 228 SER cc_start: 0.7716 (OUTLIER) cc_final: 0.7207 (t) REVERT: A 248 LYS cc_start: 0.9078 (mttt) cc_final: 0.8771 (mtpp) REVERT: A 313 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7449 (mtm-85) REVERT: B 33 ILE cc_start: 0.6576 (mp) cc_final: 0.6217 (mt) REVERT: B 67 SER cc_start: 0.9407 (m) cc_final: 0.8630 (t) REVERT: B 76 ASP cc_start: 0.7383 (t0) cc_final: 0.7097 (t0) REVERT: B 130 GLU cc_start: 0.7724 (mp0) cc_final: 0.7359 (mp0) REVERT: B 254 ASP cc_start: 0.8236 (t0) cc_final: 0.7966 (m-30) REVERT: C 32 LYS cc_start: 0.8072 (ptmm) cc_final: 0.7649 (ttpp) REVERT: E 39 GLN cc_start: 0.8253 (tp40) cc_final: 0.7869 (tp40) REVERT: E 73 ASP cc_start: 0.7340 (t0) cc_final: 0.7126 (t0) REVERT: E 192 MET cc_start: 0.7726 (ptt) cc_final: 0.7506 (ptt) REVERT: E 197 SER cc_start: 0.9285 (m) cc_final: 0.8917 (p) REVERT: E 208 SER cc_start: 0.8390 (t) cc_final: 0.8069 (p) REVERT: E 234 GLU cc_start: 0.8566 (pt0) cc_final: 0.8337 (pt0) REVERT: R 140 MET cc_start: 0.8014 (mmm) cc_final: 0.7454 (mmm) REVERT: R 369 LYS cc_start: 0.5998 (mmmt) cc_final: 0.5651 (tptt) outliers start: 29 outliers final: 25 residues processed: 192 average time/residue: 0.2438 time to fit residues: 62.6962 Evaluate side-chains 196 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 150 THR 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 78 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 208 VAL 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 80 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.152683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.120836 restraints weight = 12041.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120380 restraints weight = 11511.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122445 restraints weight = 11132.046| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.7723 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= 0.198 Angle : 0.599 12.170 12401 Z= 0.321 Chirality : 0.045 0.213 1419 Planarity : 0.004 0.070 1557 Dihedral : 5.183 55.278 1312 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.06 % Allowed : 21.84 % Favored : 75.10 % 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 (0.25), residues: 1121 helix: 1.35 (0.27), residues: 388 sheet: -0.05 (0.30), residues: 271 loop : -0.61 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS R 393 PHE 0.030 0.001 PHE R 390 TYR 0.025 0.001 TYR C 40 ARG 0.010 0.001 ARG C 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2158.15 seconds wall clock time: 39 minutes 20.76 seconds (2360.76 seconds total)