Starting phenix.real_space_refine on Mon Mar 11 08:22:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6niy_9382/03_2024/6niy_9382.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6niy_9382/03_2024/6niy_9382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6niy_9382/03_2024/6niy_9382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6niy_9382/03_2024/6niy_9382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6niy_9382/03_2024/6niy_9382.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6niy_9382/03_2024/6niy_9382.pdb" } resolution = 3.34 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 4925 2.51 5 N 1355 2.21 5 O 1391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 73": "OD1" <-> "OD2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 26": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7727 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1445 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 165} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2173 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain breaks: 2 Chain: "B" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2570 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "P" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 142 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Time building chain proxies: 4.71, per 1000 atoms: 0.61 Number of scatterers: 7727 At special positions: 0 Unit cell: (119.78, 110.24, 82.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1391 8.00 N 1355 7.00 C 4925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS P 1 " - pdb=" SG CYS P 7 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.4 seconds 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1824 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 41.9% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 3.528A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 removed outlier: 3.504A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.726A pdb=" N LEU A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.775A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.924A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.706A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 173 removed outlier: 3.544A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.513A pdb=" N ASN R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU R 204 " --> pdb=" O ILE R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 249 Processing helix chain 'R' and resid 258 through 267 removed outlier: 3.566A pdb=" N TYR R 262 " --> pdb=" O ARG R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 285 removed outlier: 3.530A pdb=" N THR R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA R 282 " --> pdb=" O ALA R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix removed outlier: 3.580A pdb=" N THR R 325 " --> pdb=" O ARG R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 removed outlier: 3.559A pdb=" N ILE R 371 " --> pdb=" O MET R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 382 through 393 removed outlier: 3.642A pdb=" N ILE R 390 " --> pdb=" O PHE R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 395 through 412 removed outlier: 3.557A pdb=" N ILE R 411 " --> pdb=" O ALA R 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 27 removed outlier: 3.839A pdb=" N ASP B 27 " --> pdb=" O LYS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.926A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.846A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 19 removed outlier: 3.557A pdb=" N LYS P 11 " --> pdb=" O CYS P 7 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 3.514A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.715A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.533A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.750A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.587A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.477A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.612A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 192 removed outlier: 7.146A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.347A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.657A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1116 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: 2.16 Time building geometry restraints manager: 2.99 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: 2501 1.34 - 1.47: 1990 1.47 - 1.59: 3318 1.59 - 1.72: 0 1.72 - 1.84: 80 Bond restraints: 7889 Sorted by residual: bond pdb=" CB ASP B 205 " pdb=" CG ASP B 205 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.23e+00 bond pdb=" CB ASN P 3 " pdb=" CG ASN P 3 " ideal model delta sigma weight residual 1.516 1.560 -0.044 2.50e-02 1.60e+03 3.10e+00 bond pdb=" CB TRP B 211 " pdb=" CG TRP B 211 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.00e+00 bond pdb=" CG LEU B 146 " pdb=" CD2 LEU B 146 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.94e+00 bond pdb=" CA SER B 72 " pdb=" CB SER B 72 " ideal model delta sigma weight residual 1.534 1.493 0.041 2.47e-02 1.64e+03 2.76e+00 ... (remaining 7884 not shown) Histogram of bond angle deviations from ideal: 98.85 - 106.24: 154 106.24 - 113.64: 4373 113.64 - 121.04: 3882 121.04 - 128.44: 2185 128.44 - 135.83: 77 Bond angle restraints: 10671 Sorted by residual: angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 130.98 -9.44 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 130.00 -8.46 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C SER P 2 " pdb=" N ASN P 3 " pdb=" CA ASN P 3 " ideal model delta sigma weight residual 122.07 127.85 -5.78 1.43e+00 4.89e-01 1.63e+01 angle pdb=" CA VAL R 272 " pdb=" CB VAL R 272 " pdb=" CG1 VAL R 272 " ideal model delta sigma weight residual 110.40 116.97 -6.57 1.70e+00 3.46e-01 1.49e+01 angle pdb=" CA PRO R 273 " pdb=" N PRO R 273 " pdb=" CD PRO R 273 " ideal model delta sigma weight residual 112.00 106.91 5.09 1.40e+00 5.10e-01 1.32e+01 ... (remaining 10666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 4128 15.88 - 31.76: 429 31.76 - 47.64: 97 47.64 - 63.52: 16 63.52 - 79.40: 7 Dihedral angle restraints: 4677 sinusoidal: 1866 harmonic: 2811 Sorted by residual: dihedral pdb=" C VAL R 272 " pdb=" N VAL R 272 " pdb=" CA VAL R 272 " pdb=" CB VAL R 272 " ideal model delta harmonic sigma weight residual -122.00 -133.58 11.58 0 2.50e+00 1.60e-01 2.14e+01 dihedral pdb=" CB CYS P 1 " pdb=" SG CYS P 1 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual -86.00 -121.79 35.79 1 1.00e+01 1.00e-02 1.81e+01 dihedral pdb=" CA ARG N 38 " pdb=" C ARG N 38 " pdb=" N GLN N 39 " pdb=" CA GLN N 39 " ideal model delta harmonic sigma weight residual 180.00 159.98 20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 4674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 842 0.060 - 0.119: 275 0.119 - 0.179: 67 0.179 - 0.238: 8 0.238 - 0.298: 6 Chirality restraints: 1198 Sorted by residual: chirality pdb=" CA VAL R 272 " pdb=" N VAL R 272 " pdb=" C VAL R 272 " pdb=" CB VAL R 272 " both_signs ideal model delta sigma weight residual False 2.44 2.14 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB VAL R 272 " pdb=" CA VAL R 272 " pdb=" CG1 VAL R 272 " pdb=" CG2 VAL R 272 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1195 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 303 " 0.056 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO R 304 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO R 304 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 304 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 17 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C GLN B 17 " -0.039 2.00e-02 2.50e+03 pdb=" O GLN B 17 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE B 18 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 236 " 0.026 2.00e-02 2.50e+03 1.29e-02 4.16e+00 pdb=" CG TRP R 236 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP R 236 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP R 236 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 236 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 236 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 236 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 236 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 236 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 236 " -0.003 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2181 2.81 - 3.33: 6867 3.33 - 3.85: 12661 3.85 - 4.38: 14463 4.38 - 4.90: 25663 Nonbonded interactions: 61835 Sorted by model distance: nonbonded pdb=" O PHE R 359 " pdb=" OG SER P 5 " model vdw 2.287 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.297 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.299 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.300 2.440 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.304 2.440 ... (remaining 61830 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.000 Extract box with map and model: 1.730 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.290 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 : 0.008 0.070 7889 Z= 0.542 Angle : 0.993 10.835 10671 Z= 0.557 Chirality : 0.064 0.298 1198 Planarity : 0.007 0.084 1346 Dihedral : 13.736 79.397 2841 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.12 % Allowed : 5.82 % Favored : 94.06 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.26), residues: 937 helix: 0.94 (0.25), residues: 370 sheet: -0.69 (0.34), residues: 221 loop : -2.30 (0.28), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP R 236 HIS 0.010 0.002 HIS A 357 PHE 0.024 0.003 PHE B 253 TYR 0.017 0.002 TYR B 59 ARG 0.006 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.8070 (m) cc_final: 0.7843 (m) REVERT: A 233 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7199 (mtpp) REVERT: A 333 ARG cc_start: 0.6793 (mtt180) cc_final: 0.5734 (ttt180) REVERT: A 334 VAL cc_start: 0.5547 (m) cc_final: 0.5298 (p) REVERT: A 358 TYR cc_start: 0.6297 (t80) cc_final: 0.5782 (t80) REVERT: A 360 TYR cc_start: 0.8788 (m-80) cc_final: 0.8291 (m-80) REVERT: A 378 ASP cc_start: 0.8536 (m-30) cc_final: 0.8027 (m-30) REVERT: A 381 ASP cc_start: 0.8654 (t70) cc_final: 0.8302 (t0) REVERT: A 392 GLU cc_start: 0.7621 (mp0) cc_final: 0.6773 (mp0) REVERT: A 394 LEU cc_start: 0.7576 (tp) cc_final: 0.7368 (tp) REVERT: N 34 MET cc_start: 0.8467 (mmp) cc_final: 0.8170 (mmm) REVERT: R 153 ILE cc_start: 0.7475 (mt) cc_final: 0.7190 (pt) REVERT: R 220 LYS cc_start: 0.5803 (mttt) cc_final: 0.5524 (mttm) REVERT: R 321 ARG cc_start: 0.7682 (ttt180) cc_final: 0.7399 (ptt180) REVERT: R 338 TYR cc_start: 0.5826 (m-10) cc_final: 0.5289 (m-80) REVERT: R 351 LEU cc_start: 0.8948 (tt) cc_final: 0.8573 (tt) REVERT: B 215 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8048 (mt-10) REVERT: G 22 GLU cc_start: 0.7382 (pt0) cc_final: 0.6774 (mt-10) REVERT: G 32 LYS cc_start: 0.8271 (mtmm) cc_final: 0.8041 (mtmm) outliers start: 1 outliers final: 1 residues processed: 227 average time/residue: 0.2547 time to fit residues: 73.0868 Evaluate side-chains 161 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 47 optimal weight: 0.0370 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.0870 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.8038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN N 5 GLN N 31 ASN R 179 GLN R 233 ASN R 395 ASN R 408 GLN B 32 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS P 3 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7889 Z= 0.194 Angle : 0.598 7.530 10671 Z= 0.323 Chirality : 0.043 0.156 1198 Planarity : 0.004 0.045 1346 Dihedral : 5.323 57.461 1051 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.38 % Allowed : 14.37 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.26), residues: 937 helix: 1.27 (0.26), residues: 369 sheet: -0.24 (0.34), residues: 222 loop : -1.99 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.007 0.001 HIS R 277 PHE 0.024 0.002 PHE R 356 TYR 0.011 0.001 TYR R 372 ARG 0.006 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.7869 (m) cc_final: 0.7641 (m) REVERT: A 233 LYS cc_start: 0.7912 (mtpt) cc_final: 0.7625 (mttt) REVERT: A 358 TYR cc_start: 0.6192 (t80) cc_final: 0.5641 (t80) REVERT: A 360 TYR cc_start: 0.8881 (m-80) cc_final: 0.8262 (m-80) REVERT: A 378 ASP cc_start: 0.8395 (m-30) cc_final: 0.7891 (m-30) REVERT: A 381 ASP cc_start: 0.8709 (t70) cc_final: 0.8484 (t0) REVERT: A 389 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7830 (mmm160) REVERT: N 34 MET cc_start: 0.8242 (mmp) cc_final: 0.8002 (mmm) REVERT: R 220 LYS cc_start: 0.5629 (mttt) cc_final: 0.5354 (mttm) REVERT: R 338 TYR cc_start: 0.5609 (m-10) cc_final: 0.5288 (m-80) REVERT: R 351 LEU cc_start: 0.9019 (tt) cc_final: 0.8693 (tt) REVERT: B 23 LYS cc_start: 0.8393 (pptt) cc_final: 0.8075 (tppt) REVERT: B 215 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7996 (mt-10) REVERT: G 20 LYS cc_start: 0.8868 (pttm) cc_final: 0.8618 (pttm) outliers start: 20 outliers final: 11 residues processed: 201 average time/residue: 0.2077 time to fit residues: 55.7937 Evaluate side-chains 181 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 170 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain P residue 15 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 0.0040 chunk 23 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 233 ASN ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 395 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7889 Z= 0.348 Angle : 0.635 7.731 10671 Z= 0.339 Chirality : 0.045 0.167 1198 Planarity : 0.004 0.040 1346 Dihedral : 5.203 59.815 1049 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.28 % Allowed : 15.91 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.26), residues: 937 helix: 1.13 (0.26), residues: 367 sheet: -0.56 (0.33), residues: 221 loop : -1.91 (0.29), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.002 PHE B 253 TYR 0.012 0.002 TYR B 105 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 171 time to evaluate : 0.915 Fit side-chains REVERT: A 40 THR cc_start: 0.7884 (m) cc_final: 0.7658 (m) REVERT: A 268 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7857 (pp20) REVERT: A 358 TYR cc_start: 0.6365 (t80) cc_final: 0.5809 (t80) REVERT: A 360 TYR cc_start: 0.8835 (m-80) cc_final: 0.8275 (m-80) REVERT: A 378 ASP cc_start: 0.8371 (m-30) cc_final: 0.7904 (m-30) REVERT: R 141 LYS cc_start: 0.5754 (mptt) cc_final: 0.5542 (mmtt) REVERT: R 220 LYS cc_start: 0.5635 (mttt) cc_final: 0.5274 (mttm) REVERT: R 346 MET cc_start: 0.5165 (tmm) cc_final: 0.4163 (mmm) REVERT: R 351 LEU cc_start: 0.8992 (tt) cc_final: 0.8613 (tt) REVERT: R 393 PHE cc_start: 0.8031 (m-80) cc_final: 0.7557 (m-80) REVERT: B 23 LYS cc_start: 0.8414 (pptt) cc_final: 0.8121 (tppt) REVERT: B 215 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7951 (mt-10) REVERT: G 20 LYS cc_start: 0.8931 (pttm) cc_final: 0.8681 (pttm) outliers start: 36 outliers final: 24 residues processed: 194 average time/residue: 0.1875 time to fit residues: 49.5240 Evaluate side-chains 182 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 15 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 408 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7889 Z= 0.233 Angle : 0.574 7.528 10671 Z= 0.306 Chirality : 0.043 0.140 1198 Planarity : 0.003 0.036 1346 Dihedral : 4.998 57.747 1049 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.16 % Allowed : 18.88 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 937 helix: 1.26 (0.26), residues: 367 sheet: -0.46 (0.33), residues: 224 loop : -1.69 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.002 PHE R 359 TYR 0.014 0.001 TYR R 191 ARG 0.006 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 165 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.7896 (m) cc_final: 0.7686 (m) REVERT: A 268 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7669 (pp20) REVERT: A 358 TYR cc_start: 0.6316 (t80) cc_final: 0.5833 (t80) REVERT: A 360 TYR cc_start: 0.8945 (m-80) cc_final: 0.8364 (m-80) REVERT: A 378 ASP cc_start: 0.8341 (m-30) cc_final: 0.7877 (m-30) REVERT: A 392 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6976 (mt-10) REVERT: R 220 LYS cc_start: 0.5742 (mttt) cc_final: 0.5362 (mttm) REVERT: R 337 MET cc_start: 0.7235 (ppp) cc_final: 0.6647 (ptt) REVERT: R 346 MET cc_start: 0.5106 (tmm) cc_final: 0.3983 (mmm) REVERT: R 351 LEU cc_start: 0.8958 (tt) cc_final: 0.8627 (tt) REVERT: R 357 VAL cc_start: 0.7745 (OUTLIER) cc_final: 0.7497 (t) REVERT: B 23 LYS cc_start: 0.8379 (pptt) cc_final: 0.8176 (tppt) REVERT: B 215 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8018 (mt-10) REVERT: G 19 LEU cc_start: 0.8507 (mm) cc_final: 0.8306 (mm) REVERT: G 20 LYS cc_start: 0.8904 (pttm) cc_final: 0.8636 (pttm) REVERT: G 32 LYS cc_start: 0.8142 (mtmm) cc_final: 0.7940 (mtmm) REVERT: G 42 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7225 (pt0) REVERT: P 11 LYS cc_start: 0.7736 (tttm) cc_final: 0.7307 (ttmm) outliers start: 35 outliers final: 28 residues processed: 186 average time/residue: 0.1995 time to fit residues: 50.3109 Evaluate side-chains 185 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain P residue 15 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 395 ASN R 408 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7889 Z= 0.173 Angle : 0.527 7.538 10671 Z= 0.279 Chirality : 0.041 0.133 1198 Planarity : 0.003 0.036 1346 Dihedral : 5.022 80.304 1049 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.99 % Allowed : 19.60 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 937 helix: 1.47 (0.26), residues: 372 sheet: -0.31 (0.32), residues: 227 loop : -1.50 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.006 0.001 HIS R 377 PHE 0.026 0.001 PHE R 224 TYR 0.013 0.001 TYR R 191 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 167 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7426 (pp20) REVERT: A 358 TYR cc_start: 0.6280 (t80) cc_final: 0.5832 (t80) REVERT: A 360 TYR cc_start: 0.8982 (m-80) cc_final: 0.8568 (m-80) REVERT: A 378 ASP cc_start: 0.8295 (m-30) cc_final: 0.7854 (m-30) REVERT: R 220 LYS cc_start: 0.5650 (mttt) cc_final: 0.5282 (mttm) REVERT: R 291 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.6043 (tt) REVERT: R 337 MET cc_start: 0.7111 (ppp) cc_final: 0.6432 (ptt) REVERT: R 346 MET cc_start: 0.5099 (tmm) cc_final: 0.3920 (mmm) REVERT: R 351 LEU cc_start: 0.8993 (tt) cc_final: 0.8665 (tt) REVERT: R 357 VAL cc_start: 0.7703 (OUTLIER) cc_final: 0.7448 (t) REVERT: B 37 ILE cc_start: 0.7641 (pt) cc_final: 0.7339 (pt) REVERT: B 215 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8080 (mt-10) REVERT: B 280 LYS cc_start: 0.8462 (tttt) cc_final: 0.8173 (ttpt) REVERT: G 20 LYS cc_start: 0.8896 (pttm) cc_final: 0.8632 (pttm) REVERT: G 32 LYS cc_start: 0.8143 (mtmm) cc_final: 0.7923 (mtmm) REVERT: G 42 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7205 (pt0) REVERT: P 11 LYS cc_start: 0.7831 (tttm) cc_final: 0.7298 (ttmm) outliers start: 42 outliers final: 26 residues processed: 194 average time/residue: 0.2010 time to fit residues: 53.3806 Evaluate side-chains 183 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain P residue 15 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 156 HIS ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 412 GLN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7889 Z= 0.169 Angle : 0.529 8.043 10671 Z= 0.278 Chirality : 0.041 0.133 1198 Planarity : 0.003 0.045 1346 Dihedral : 4.863 74.958 1049 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.87 % Allowed : 20.43 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.27), residues: 937 helix: 1.65 (0.26), residues: 373 sheet: -0.36 (0.32), residues: 223 loop : -1.39 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.006 0.001 HIS R 377 PHE 0.021 0.001 PHE R 359 TYR 0.012 0.001 TYR R 191 ARG 0.002 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 153 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7366 (pp20) REVERT: A 358 TYR cc_start: 0.6298 (t80) cc_final: 0.5873 (t80) REVERT: A 360 TYR cc_start: 0.8979 (m-80) cc_final: 0.8582 (m-80) REVERT: A 378 ASP cc_start: 0.8237 (m-30) cc_final: 0.7785 (m-30) REVERT: R 187 MET cc_start: 0.7637 (tpt) cc_final: 0.7030 (tpt) REVERT: R 220 LYS cc_start: 0.5395 (mttt) cc_final: 0.5021 (mttm) REVERT: R 291 LEU cc_start: 0.6308 (tp) cc_final: 0.6004 (tt) REVERT: R 337 MET cc_start: 0.7078 (ppp) cc_final: 0.6358 (ptt) REVERT: R 346 MET cc_start: 0.5122 (tmm) cc_final: 0.4213 (mmm) REVERT: R 351 LEU cc_start: 0.9056 (tt) cc_final: 0.8694 (tt) REVERT: R 357 VAL cc_start: 0.7765 (OUTLIER) cc_final: 0.7500 (t) REVERT: B 37 ILE cc_start: 0.7719 (pt) cc_final: 0.7374 (pt) REVERT: B 101 MET cc_start: 0.7682 (mmm) cc_final: 0.7407 (mmm) REVERT: B 217 MET cc_start: 0.7788 (ptp) cc_final: 0.7510 (tpt) REVERT: G 20 LYS cc_start: 0.8886 (pttm) cc_final: 0.8616 (pttm) REVERT: G 42 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7222 (pt0) REVERT: P 11 LYS cc_start: 0.7677 (tttm) cc_final: 0.7095 (ttmm) outliers start: 41 outliers final: 31 residues processed: 180 average time/residue: 0.1939 time to fit residues: 47.6871 Evaluate side-chains 181 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain P residue 3 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 6.9990 chunk 10 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN P 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7889 Z= 0.312 Angle : 0.611 8.328 10671 Z= 0.320 Chirality : 0.044 0.141 1198 Planarity : 0.004 0.037 1346 Dihedral : 5.138 78.750 1049 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.99 % Allowed : 21.73 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.27), residues: 937 helix: 1.58 (0.26), residues: 371 sheet: -0.52 (0.32), residues: 224 loop : -1.37 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 290 HIS 0.011 0.001 HIS R 377 PHE 0.023 0.002 PHE R 359 TYR 0.013 0.002 TYR R 191 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 151 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7409 (pp20) REVERT: A 358 TYR cc_start: 0.6367 (t80) cc_final: 0.5816 (t80) REVERT: A 360 TYR cc_start: 0.8941 (m-80) cc_final: 0.8357 (m-80) REVERT: A 378 ASP cc_start: 0.8265 (m-30) cc_final: 0.7854 (m-30) REVERT: R 187 MET cc_start: 0.7605 (tpt) cc_final: 0.7037 (tpt) REVERT: R 220 LYS cc_start: 0.5693 (mttt) cc_final: 0.5327 (mttm) REVERT: R 291 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.6042 (tt) REVERT: R 306 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7782 (mmt) REVERT: R 351 LEU cc_start: 0.9101 (tt) cc_final: 0.8772 (tt) REVERT: R 357 VAL cc_start: 0.7839 (OUTLIER) cc_final: 0.7587 (t) REVERT: R 367 MET cc_start: 0.6563 (tmm) cc_final: 0.6355 (tmm) REVERT: B 37 ILE cc_start: 0.7802 (pt) cc_final: 0.7477 (pt) REVERT: B 217 MET cc_start: 0.7967 (ptp) cc_final: 0.7586 (tpt) REVERT: G 20 LYS cc_start: 0.8883 (pttm) cc_final: 0.8608 (pttm) REVERT: G 42 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7248 (pt0) REVERT: P 11 LYS cc_start: 0.7666 (tttm) cc_final: 0.7090 (ttmm) outliers start: 42 outliers final: 31 residues processed: 177 average time/residue: 0.2016 time to fit residues: 49.5786 Evaluate side-chains 182 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain P residue 3 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 70 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 179 GLN ** R 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7889 Z= 0.161 Angle : 0.551 8.602 10671 Z= 0.287 Chirality : 0.041 0.130 1198 Planarity : 0.003 0.036 1346 Dihedral : 4.847 74.462 1049 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.28 % Allowed : 22.80 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.27), residues: 937 helix: 1.76 (0.27), residues: 372 sheet: -0.32 (0.33), residues: 221 loop : -1.24 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 236 HIS 0.010 0.001 HIS R 377 PHE 0.025 0.001 PHE R 359 TYR 0.012 0.001 TYR R 191 ARG 0.002 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7390 (pp20) REVERT: A 358 TYR cc_start: 0.6336 (t80) cc_final: 0.5837 (t80) REVERT: A 360 TYR cc_start: 0.8958 (m-80) cc_final: 0.8535 (m-80) REVERT: A 378 ASP cc_start: 0.8207 (m-30) cc_final: 0.7782 (m-30) REVERT: R 187 MET cc_start: 0.7708 (tpt) cc_final: 0.7263 (tpt) REVERT: R 220 LYS cc_start: 0.5493 (mttt) cc_final: 0.5122 (mttm) REVERT: R 291 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5939 (tt) REVERT: R 306 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7758 (mmt) REVERT: R 351 LEU cc_start: 0.9110 (tt) cc_final: 0.8757 (tt) REVERT: R 357 VAL cc_start: 0.7752 (OUTLIER) cc_final: 0.7496 (t) REVERT: B 37 ILE cc_start: 0.7891 (pt) cc_final: 0.7551 (pt) REVERT: B 101 MET cc_start: 0.7769 (mmm) cc_final: 0.7483 (mmm) REVERT: B 215 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7796 (mt-10) REVERT: B 217 MET cc_start: 0.7830 (ptp) cc_final: 0.7515 (tpt) REVERT: B 280 LYS cc_start: 0.8483 (tttt) cc_final: 0.8052 (ttpt) REVERT: G 20 LYS cc_start: 0.8875 (pttm) cc_final: 0.8587 (pttm) REVERT: G 42 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7051 (pt0) REVERT: P 11 LYS cc_start: 0.7592 (tttm) cc_final: 0.6970 (ttmm) outliers start: 36 outliers final: 22 residues processed: 173 average time/residue: 0.1937 time to fit residues: 45.6128 Evaluate side-chains 173 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain P residue 3 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 85 optimal weight: 0.0570 chunk 50 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 75 optimal weight: 0.0060 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 0.0000 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 HIS ** R 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN P 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7889 Z= 0.149 Angle : 0.541 8.861 10671 Z= 0.282 Chirality : 0.040 0.129 1198 Planarity : 0.003 0.036 1346 Dihedral : 4.630 70.914 1049 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.21 % Allowed : 23.28 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.27), residues: 937 helix: 1.88 (0.27), residues: 371 sheet: -0.15 (0.33), residues: 224 loop : -1.17 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 236 HIS 0.008 0.001 HIS R 377 PHE 0.028 0.001 PHE R 224 TYR 0.012 0.001 TYR R 191 ARG 0.002 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7372 (pp20) REVERT: A 358 TYR cc_start: 0.6305 (t80) cc_final: 0.5812 (t80) REVERT: A 360 TYR cc_start: 0.8974 (m-80) cc_final: 0.8613 (m-80) REVERT: R 187 MET cc_start: 0.7692 (tpt) cc_final: 0.7241 (tpt) REVERT: R 220 LYS cc_start: 0.5403 (mttt) cc_final: 0.5074 (mttm) REVERT: R 291 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5860 (tt) REVERT: R 306 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7737 (mmt) REVERT: R 351 LEU cc_start: 0.9098 (tt) cc_final: 0.8782 (tt) REVERT: R 357 VAL cc_start: 0.7721 (OUTLIER) cc_final: 0.7456 (t) REVERT: B 37 ILE cc_start: 0.7926 (pt) cc_final: 0.7612 (pt) REVERT: B 101 MET cc_start: 0.7690 (mmm) cc_final: 0.7429 (mmm) REVERT: B 215 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7865 (mt-10) REVERT: B 217 MET cc_start: 0.7874 (ptp) cc_final: 0.7509 (tpt) REVERT: G 20 LYS cc_start: 0.8860 (pttm) cc_final: 0.8574 (pttm) REVERT: G 42 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: P 11 LYS cc_start: 0.7543 (tttm) cc_final: 0.6890 (ttmm) outliers start: 27 outliers final: 16 residues processed: 167 average time/residue: 0.1889 time to fit residues: 43.6005 Evaluate side-chains 165 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 31 GLN ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7889 Z= 0.186 Angle : 0.549 8.823 10671 Z= 0.286 Chirality : 0.041 0.130 1198 Planarity : 0.003 0.036 1346 Dihedral : 4.637 69.709 1049 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.56 % Allowed : 23.75 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.27), residues: 937 helix: 1.78 (0.27), residues: 375 sheet: -0.23 (0.34), residues: 221 loop : -1.11 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 236 HIS 0.013 0.001 HIS R 377 PHE 0.027 0.001 PHE R 359 TYR 0.013 0.001 TYR R 191 ARG 0.002 0.000 ARG N 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7414 (pp20) REVERT: A 358 TYR cc_start: 0.6340 (t80) cc_final: 0.5835 (t80) REVERT: A 360 TYR cc_start: 0.8932 (m-80) cc_final: 0.8583 (m-80) REVERT: R 187 MET cc_start: 0.7705 (tpt) cc_final: 0.7239 (tpt) REVERT: R 220 LYS cc_start: 0.5365 (mttt) cc_final: 0.5045 (mttm) REVERT: R 291 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5844 (tt) REVERT: R 306 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7746 (mmt) REVERT: R 351 LEU cc_start: 0.9098 (tt) cc_final: 0.8820 (tt) REVERT: R 357 VAL cc_start: 0.7744 (OUTLIER) cc_final: 0.7479 (t) REVERT: B 37 ILE cc_start: 0.8031 (pt) cc_final: 0.7711 (pt) REVERT: B 215 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7833 (mt-10) REVERT: B 217 MET cc_start: 0.7901 (ptp) cc_final: 0.7531 (tpt) REVERT: G 20 LYS cc_start: 0.8875 (pttm) cc_final: 0.8598 (pttm) REVERT: G 42 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7508 (pt0) REVERT: P 11 LYS cc_start: 0.7575 (tttm) cc_final: 0.6889 (ttmm) outliers start: 30 outliers final: 23 residues processed: 160 average time/residue: 0.1914 time to fit residues: 42.1464 Evaluate side-chains 170 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.148235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.118724 restraints weight = 11012.936| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.47 r_work: 0.3502 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 7889 Z= 0.269 Angle : 0.939 59.192 10671 Z= 0.539 Chirality : 0.041 0.252 1198 Planarity : 0.003 0.038 1346 Dihedral : 4.643 69.736 1049 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.68 % Allowed : 23.63 % Favored : 72.68 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.27), residues: 937 helix: 1.78 (0.27), residues: 375 sheet: -0.24 (0.34), residues: 221 loop : -1.11 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 236 HIS 0.011 0.001 HIS R 377 PHE 0.021 0.001 PHE R 359 TYR 0.012 0.001 TYR R 191 ARG 0.002 0.000 ARG N 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2149.05 seconds wall clock time: 39 minutes 31.35 seconds (2371.35 seconds total)