Starting phenix.real_space_refine on Tue Feb 13 22:47:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9y_20278/02_2024/6p9y_20278.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9y_20278/02_2024/6p9y_20278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9y_20278/02_2024/6p9y_20278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9y_20278/02_2024/6p9y_20278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9y_20278/02_2024/6p9y_20278.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9y_20278/02_2024/6p9y_20278.pdb" } resolution = 3.01 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 49 5.16 5 C 5099 2.51 5 N 1386 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 262": "OE1" <-> "OE2" Residue "R ARG 288": "NH1" <-> "NH2" Residue "R ARG 350": "NH1" <-> "NH2" Residue "R ARG 353": "NH1" <-> "NH2" Residue "R GLU 374": "OE1" <-> "OE2" Residue "R ARG 379": "NH1" <-> "NH2" Residue "R GLU 385": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7994 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1645 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} 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: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 2143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2143 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 6, 'TRANS': 251} Chain breaks: 2 Time building chain proxies: 4.62, per 1000 atoms: 0.58 Number of scatterers: 7994 At special positions: 0 Unit cell: (80.948, 96.642, 142.898, 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 49 16.00 O 1460 8.00 N 1386 7.00 C 5099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.5 seconds 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1874 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 40.7% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.579A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.664A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 4.275A pdb=" N ASP A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 removed outlier: 3.640A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.966A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 4.439A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.646A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 37 through 42 Processing helix chain 'G' and resid 44 through 48 removed outlier: 3.922A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.680A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.683A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.803A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 27 removed outlier: 3.653A pdb=" N PHE P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP P 8 " --> pdb=" O GLY P 4 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 164 removed outlier: 3.622A pdb=" N LEU R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR R 158 " --> pdb=" O LYS R 154 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL R 159 " --> pdb=" O ALA R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 178 removed outlier: 3.747A pdb=" N THR R 170 " --> pdb=" O VAL R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 211 removed outlier: 3.674A pdb=" N TRP R 208 " --> pdb=" O PHE R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.980A pdb=" N VAL R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE R 232 " --> pdb=" O ALA R 228 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE R 245 " --> pdb=" O TYR R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 274 removed outlier: 3.697A pdb=" N ILE R 271 " --> pdb=" O TYR R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 289 Processing helix chain 'R' and resid 302 through 337 removed outlier: 4.001A pdb=" N VAL R 308 " --> pdb=" O ALA R 304 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.583A pdb=" N ILE R 317 " --> pdb=" O VAL R 313 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL R 322 " --> pdb=" O MET R 318 " (cutoff:3.500A) Processing helix chain 'R' and resid 347 through 363 Proline residue: R 360 - end of helix Processing helix chain 'R' and resid 364 through 367 Processing helix chain 'R' and resid 378 through 386 removed outlier: 3.761A pdb=" N VAL R 383 " --> pdb=" O ARG R 379 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 401 Processing helix chain 'R' and resid 404 through 417 removed outlier: 3.647A pdb=" N GLU R 410 " --> pdb=" O GLU R 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.303A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.658A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.334A 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: 5.757A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.750A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.891A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.574A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.979A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.123A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 17 through 20 368 hydrogen bonds defined for protein. 1041 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: 2.51 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2586 1.35 - 1.47: 2005 1.47 - 1.59: 3510 1.59 - 1.71: 0 1.71 - 1.83: 69 Bond restraints: 8170 Sorted by residual: bond pdb=" C ASP B 38 " pdb=" N PRO B 39 " ideal model delta sigma weight residual 1.330 1.378 -0.048 1.25e-02 6.40e+03 1.45e+01 bond pdb=" N ILE B 270 " pdb=" CA ILE B 270 " ideal model delta sigma weight residual 1.459 1.493 -0.035 9.10e-03 1.21e+04 1.44e+01 bond pdb=" N VAL B 307 " pdb=" CA VAL B 307 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.15e+01 bond pdb=" N ILE B 37 " pdb=" CA ILE B 37 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N ILE B 80 " pdb=" CA ILE B 80 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.17e-02 7.31e+03 9.17e+00 ... (remaining 8165 not shown) Histogram of bond angle deviations from ideal: 100.19 - 107.01: 181 107.01 - 113.84: 4537 113.84 - 120.66: 3461 120.66 - 127.49: 2796 127.49 - 134.31: 83 Bond angle restraints: 11058 Sorted by residual: angle pdb=" C ASP B 38 " pdb=" N PRO B 39 " pdb=" CA PRO B 39 " ideal model delta sigma weight residual 120.21 125.92 -5.71 9.60e-01 1.09e+00 3.53e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.47 108.75 4.72 1.01e+00 9.80e-01 2.18e+01 angle pdb=" N ASP B 290 " pdb=" CA ASP B 290 " pdb=" C ASP B 290 " ideal model delta sigma weight residual 111.28 106.73 4.55 1.09e+00 8.42e-01 1.74e+01 angle pdb=" CA GLY B 272 " pdb=" C GLY B 272 " pdb=" O GLY B 272 " ideal model delta sigma weight residual 121.58 118.03 3.55 9.00e-01 1.23e+00 1.56e+01 angle pdb=" N ILE G 9 " pdb=" CA ILE G 9 " pdb=" C ILE G 9 " ideal model delta sigma weight residual 113.42 108.90 4.52 1.17e+00 7.31e-01 1.50e+01 ... (remaining 11053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 4420 17.07 - 34.13: 325 34.13 - 51.20: 59 51.20 - 68.27: 9 68.27 - 85.34: 5 Dihedral angle restraints: 4818 sinusoidal: 1916 harmonic: 2902 Sorted by residual: dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 42.60 50.40 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" C HIS B 311 " pdb=" N HIS B 311 " pdb=" CA HIS B 311 " pdb=" CB HIS B 311 " ideal model delta harmonic sigma weight residual -122.60 -131.68 9.08 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" CA ASP B 186 " pdb=" CB ASP B 186 " pdb=" CG ASP B 186 " pdb=" OD1 ASP B 186 " ideal model delta sinusoidal sigma weight residual -30.00 -90.69 60.69 1 2.00e+01 2.50e-03 1.23e+01 ... (remaining 4815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 968 0.053 - 0.105: 193 0.105 - 0.158: 43 0.158 - 0.210: 11 0.210 - 0.263: 9 Chirality restraints: 1224 Sorted by residual: chirality pdb=" CA LYS A 280 " pdb=" N LYS A 280 " pdb=" C LYS A 280 " pdb=" CB LYS A 280 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA HIS B 311 " pdb=" N HIS B 311 " pdb=" C HIS B 311 " pdb=" CB HIS B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1221 not shown) Planarity restraints: 1400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 297 " 0.025 2.00e-02 2.50e+03 1.92e-02 9.22e+00 pdb=" CG TRP R 297 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP R 297 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP R 297 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 297 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 297 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP R 297 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 297 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 297 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP R 297 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C ILE R 205 " 0.026 2.00e-02 2.50e+03 pdb=" O ILE R 205 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS R 206 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 311 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO R 312 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO R 312 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 312 " 0.019 5.00e-02 4.00e+02 ... (remaining 1397 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1779 2.78 - 3.31: 7554 3.31 - 3.84: 13124 3.84 - 4.37: 17133 4.37 - 4.90: 28362 Nonbonded interactions: 67952 Sorted by model distance: nonbonded pdb=" NE2 HIS A 362 " pdb=" OD2 ASP A 378 " model vdw 2.246 2.520 nonbonded pdb=" ND2 ASN R 320 " pdb=" O PHE R 362 " model vdw 2.257 2.520 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.262 2.440 nonbonded pdb=" O ASN B 293 " pdb=" ND2 ASN B 293 " model vdw 2.287 2.520 nonbonded pdb=" OE1 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.293 2.440 ... (remaining 67947 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=0.00 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: 1.300 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: 5.270 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.420 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 0.048 8170 Z= 0.326 Angle : 0.681 6.926 11058 Z= 0.469 Chirality : 0.051 0.263 1224 Planarity : 0.003 0.034 1400 Dihedral : 12.481 85.336 2935 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.81 % Allowed : 3.59 % Favored : 95.60 % 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: -4.06 (0.23), residues: 974 helix: -3.63 (0.18), residues: 352 sheet: -2.19 (0.33), residues: 213 loop : -1.82 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP R 297 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.016 0.001 TYR R 157 ARG 0.004 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6727 (tm-30) REVERT: A 20 ARG cc_start: 0.7299 (ttp-110) cc_final: 0.7005 (ttp80) REVERT: A 34 LYS cc_start: 0.8235 (tttp) cc_final: 0.7970 (ttpt) REVERT: A 209 GLU cc_start: 0.7185 (tt0) cc_final: 0.6717 (tt0) REVERT: B 186 ASP cc_start: 0.7990 (p0) cc_final: 0.7490 (p0) REVERT: N 46 GLU cc_start: 0.8144 (pt0) cc_final: 0.7820 (mt-10) REVERT: R 378 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7659 (mtpp) REVERT: R 379 ARG cc_start: 0.7571 (mmm160) cc_final: 0.7362 (mmm160) outliers start: 7 outliers final: 3 residues processed: 146 average time/residue: 0.3041 time to fit residues: 55.4385 Evaluate side-chains 107 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.1980 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 29 GLN A 278 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 35 ASN B 88 ASN B 293 ASN B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN N 123 GLN P 1 HIS P 16 GLN R 240 ASN R 333 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8170 Z= 0.194 Angle : 0.536 6.220 11058 Z= 0.290 Chirality : 0.042 0.143 1224 Planarity : 0.004 0.039 1400 Dihedral : 4.857 50.038 1098 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.62 % Allowed : 8.00 % Favored : 90.38 % 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: -2.19 (0.25), residues: 974 helix: -1.14 (0.26), residues: 357 sheet: -1.68 (0.34), residues: 214 loop : -1.40 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 297 HIS 0.005 0.001 HIS B 311 PHE 0.020 0.001 PHE A 212 TYR 0.024 0.001 TYR R 157 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8011 (tttp) cc_final: 0.7772 (ttpt) REVERT: A 389 ARG cc_start: 0.6987 (ttm-80) cc_final: 0.6706 (ttm-80) REVERT: B 186 ASP cc_start: 0.8024 (p0) cc_final: 0.7666 (p0) REVERT: N 28 THR cc_start: 0.8258 (m) cc_final: 0.8044 (p) REVERT: N 46 GLU cc_start: 0.8038 (pt0) cc_final: 0.7785 (mt-10) REVERT: R 190 MET cc_start: 0.6866 (mtp) cc_final: 0.6664 (mtt) REVERT: R 379 ARG cc_start: 0.7481 (mmm160) cc_final: 0.7277 (mmm160) outliers start: 14 outliers final: 7 residues processed: 126 average time/residue: 0.2607 time to fit residues: 42.6888 Evaluate side-chains 111 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 297 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 17 GLN B 88 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8170 Z= 0.192 Angle : 0.503 5.679 11058 Z= 0.271 Chirality : 0.041 0.137 1224 Planarity : 0.003 0.037 1400 Dihedral : 4.379 19.318 1096 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.09 % Allowed : 11.36 % Favored : 86.56 % 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: -1.42 (0.26), residues: 974 helix: -0.26 (0.27), residues: 361 sheet: -1.54 (0.34), residues: 211 loop : -1.05 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.001 PHE A 212 TYR 0.021 0.001 TYR R 157 ARG 0.007 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7175 (tttm) cc_final: 0.6969 (mmtt) REVERT: A 342 ARG cc_start: 0.7600 (ttt180) cc_final: 0.7006 (ttp-170) REVERT: A 389 ARG cc_start: 0.7004 (ttm-80) cc_final: 0.6668 (ttm-80) REVERT: B 186 ASP cc_start: 0.8176 (p0) cc_final: 0.7867 (p0) REVERT: N 46 GLU cc_start: 0.8017 (pt0) cc_final: 0.7758 (mt-10) REVERT: R 379 ARG cc_start: 0.7457 (mmm160) cc_final: 0.7252 (mmm160) outliers start: 18 outliers final: 10 residues processed: 127 average time/residue: 0.3381 time to fit residues: 53.5736 Evaluate side-chains 119 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 297 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 45 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN B 88 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8170 Z= 0.177 Angle : 0.484 5.741 11058 Z= 0.261 Chirality : 0.041 0.135 1224 Planarity : 0.003 0.035 1400 Dihedral : 4.234 19.930 1095 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.43 % Allowed : 12.98 % Favored : 84.59 % 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: -0.85 (0.27), residues: 974 helix: 0.28 (0.27), residues: 363 sheet: -1.29 (0.34), residues: 211 loop : -0.77 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE A 212 TYR 0.020 0.001 TYR R 157 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7159 (tttm) cc_final: 0.6930 (mmtt) REVERT: A 230 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7696 (mt-10) REVERT: A 342 ARG cc_start: 0.7558 (ttt180) cc_final: 0.6959 (ttp-110) REVERT: A 389 ARG cc_start: 0.7032 (ttm-80) cc_final: 0.6671 (ttm-80) REVERT: B 105 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8604 (t80) REVERT: B 186 ASP cc_start: 0.8156 (p0) cc_final: 0.7903 (p0) REVERT: N 46 GLU cc_start: 0.7972 (pt0) cc_final: 0.7703 (mt-10) REVERT: R 379 ARG cc_start: 0.7464 (mmm160) cc_final: 0.7255 (mmm160) outliers start: 21 outliers final: 13 residues processed: 120 average time/residue: 0.2642 time to fit residues: 41.0496 Evaluate side-chains 124 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain R residue 332 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.0010 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 213 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8170 Z= 0.173 Angle : 0.471 5.748 11058 Z= 0.255 Chirality : 0.040 0.132 1224 Planarity : 0.003 0.033 1400 Dihedral : 4.167 20.134 1095 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.09 % Allowed : 14.14 % Favored : 83.78 % 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: -0.53 (0.27), residues: 974 helix: 0.62 (0.28), residues: 364 sheet: -1.16 (0.34), residues: 211 loop : -0.63 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE A 212 TYR 0.019 0.001 TYR R 157 ARG 0.002 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6529 (mtm110) cc_final: 0.6167 (mtm-85) REVERT: A 24 LYS cc_start: 0.7053 (tttm) cc_final: 0.6762 (mtmm) REVERT: A 27 GLU cc_start: 0.7459 (tp30) cc_final: 0.6760 (mp0) REVERT: A 342 ARG cc_start: 0.7566 (ttt180) cc_final: 0.7007 (ttp-170) REVERT: A 389 ARG cc_start: 0.7024 (ttm-80) cc_final: 0.6648 (ttm-80) REVERT: B 98 SER cc_start: 0.8452 (m) cc_final: 0.8100 (t) REVERT: B 105 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.8641 (t80) REVERT: B 186 ASP cc_start: 0.8150 (p0) cc_final: 0.7923 (p0) REVERT: N 46 GLU cc_start: 0.7964 (pt0) cc_final: 0.7672 (mt-10) REVERT: R 378 LYS cc_start: 0.7735 (ttmt) cc_final: 0.7516 (mtpp) outliers start: 18 outliers final: 12 residues processed: 124 average time/residue: 0.2546 time to fit residues: 40.8553 Evaluate side-chains 122 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 297 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.0980 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 213 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8170 Z= 0.170 Angle : 0.472 5.652 11058 Z= 0.254 Chirality : 0.041 0.133 1224 Planarity : 0.003 0.033 1400 Dihedral : 4.140 20.237 1095 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.20 % Allowed : 14.02 % Favored : 83.78 % 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: -0.31 (0.27), residues: 974 helix: 0.84 (0.28), residues: 364 sheet: -1.08 (0.33), residues: 212 loop : -0.53 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE A 212 TYR 0.019 0.001 TYR R 157 ARG 0.002 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6494 (mtm110) cc_final: 0.6135 (mtm-85) REVERT: A 24 LYS cc_start: 0.7060 (tttm) cc_final: 0.6759 (mtmm) REVERT: A 27 GLU cc_start: 0.7446 (tp30) cc_final: 0.6772 (mp0) REVERT: A 32 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8259 (ttmt) REVERT: A 342 ARG cc_start: 0.7562 (ttt180) cc_final: 0.7002 (ttp-170) REVERT: A 389 ARG cc_start: 0.7059 (ttm-80) cc_final: 0.6771 (ttm-80) REVERT: B 98 SER cc_start: 0.8435 (m) cc_final: 0.8066 (t) REVERT: B 105 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8543 (t80) REVERT: B 186 ASP cc_start: 0.8114 (p0) cc_final: 0.7904 (p0) REVERT: N 46 GLU cc_start: 0.7948 (pt0) cc_final: 0.7660 (mt-10) REVERT: R 378 LYS cc_start: 0.7725 (ttmt) cc_final: 0.7523 (mtpp) outliers start: 19 outliers final: 15 residues processed: 126 average time/residue: 0.2833 time to fit residues: 45.6900 Evaluate side-chains 126 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain R residue 332 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 92 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN A 41 HIS A 371 ASN B 88 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8170 Z= 0.169 Angle : 0.470 5.925 11058 Z= 0.254 Chirality : 0.041 0.134 1224 Planarity : 0.003 0.033 1400 Dihedral : 4.121 20.375 1095 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.20 % Allowed : 15.06 % Favored : 82.73 % 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: -0.16 (0.27), residues: 974 helix: 0.94 (0.28), residues: 366 sheet: -0.97 (0.34), residues: 211 loop : -0.44 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE A 212 TYR 0.019 0.001 TYR R 157 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6547 (mtm110) cc_final: 0.6202 (mtm-85) REVERT: A 24 LYS cc_start: 0.7040 (tttm) cc_final: 0.6706 (mtmm) REVERT: A 342 ARG cc_start: 0.7544 (ttt180) cc_final: 0.6981 (ttp-170) REVERT: B 98 SER cc_start: 0.8438 (m) cc_final: 0.8098 (t) REVERT: B 105 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8549 (t80) REVERT: B 186 ASP cc_start: 0.8120 (p0) cc_final: 0.7914 (p0) REVERT: N 46 GLU cc_start: 0.7946 (pt0) cc_final: 0.7656 (mt-10) REVERT: R 378 LYS cc_start: 0.7726 (ttmt) cc_final: 0.7522 (mtpp) outliers start: 19 outliers final: 17 residues processed: 124 average time/residue: 0.2568 time to fit residues: 41.3336 Evaluate side-chains 122 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 332 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.0970 chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** B 293 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: 0.7884 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8170 Z= 0.160 Angle : 0.474 7.008 11058 Z= 0.255 Chirality : 0.041 0.133 1224 Planarity : 0.003 0.032 1400 Dihedral : 4.091 20.392 1095 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.32 % Allowed : 14.83 % Favored : 82.85 % 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: -0.08 (0.27), residues: 974 helix: 0.96 (0.28), residues: 370 sheet: -0.83 (0.34), residues: 209 loop : -0.44 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 297 HIS 0.006 0.001 HIS A 220 PHE 0.018 0.001 PHE A 212 TYR 0.019 0.001 TYR R 157 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7076 (tttm) cc_final: 0.6869 (mmtm) REVERT: A 213 GLN cc_start: 0.8195 (tt0) cc_final: 0.7815 (tt0) REVERT: A 342 ARG cc_start: 0.7532 (ttt180) cc_final: 0.6977 (ttp-170) REVERT: A 389 ARG cc_start: 0.7071 (ttm-80) cc_final: 0.6678 (ttm-80) REVERT: B 98 SER cc_start: 0.8431 (m) cc_final: 0.8102 (t) REVERT: B 105 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.8543 (t80) REVERT: N 46 GLU cc_start: 0.7942 (pt0) cc_final: 0.7651 (mt-10) REVERT: R 378 LYS cc_start: 0.7733 (ttmt) cc_final: 0.7531 (mtpp) outliers start: 20 outliers final: 18 residues processed: 122 average time/residue: 0.2603 time to fit residues: 41.2787 Evaluate side-chains 124 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 332 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 0.2980 chunk 56 optimal weight: 0.0470 chunk 91 optimal weight: 0.1980 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8170 Z= 0.127 Angle : 0.461 6.524 11058 Z= 0.249 Chirality : 0.040 0.138 1224 Planarity : 0.003 0.031 1400 Dihedral : 3.975 19.994 1095 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.32 % Allowed : 15.06 % Favored : 82.62 % 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: 0.08 (0.28), residues: 974 helix: 1.09 (0.28), residues: 371 sheet: -0.71 (0.34), residues: 215 loop : -0.35 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 297 HIS 0.005 0.001 HIS A 220 PHE 0.017 0.001 PHE A 212 TYR 0.018 0.001 TYR R 157 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6534 (mtm110) cc_final: 0.6122 (mtm-85) REVERT: A 24 LYS cc_start: 0.7087 (tttm) cc_final: 0.6864 (mmtm) REVERT: A 32 LYS cc_start: 0.8373 (ttmm) cc_final: 0.8135 (ttmt) REVERT: A 342 ARG cc_start: 0.7481 (ttt180) cc_final: 0.6967 (ttp-170) REVERT: A 389 ARG cc_start: 0.7062 (ttm-80) cc_final: 0.6668 (ttm-80) REVERT: B 98 SER cc_start: 0.8407 (m) cc_final: 0.8090 (t) REVERT: B 105 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8586 (t80) REVERT: N 46 GLU cc_start: 0.7875 (pt0) cc_final: 0.7636 (mt-10) REVERT: R 257 GLU cc_start: 0.6738 (tp30) cc_final: 0.6479 (tt0) REVERT: R 378 LYS cc_start: 0.7739 (ttmt) cc_final: 0.7529 (mtpp) outliers start: 20 outliers final: 18 residues processed: 129 average time/residue: 0.2772 time to fit residues: 45.7817 Evaluate side-chains 125 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain R residue 332 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8170 Z= 0.147 Angle : 0.466 6.282 11058 Z= 0.251 Chirality : 0.040 0.136 1224 Planarity : 0.003 0.032 1400 Dihedral : 3.992 19.690 1095 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.09 % Allowed : 15.18 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.28), residues: 974 helix: 1.17 (0.28), residues: 371 sheet: -0.68 (0.34), residues: 216 loop : -0.33 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 297 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.001 PHE A 212 TYR 0.020 0.001 TYR N 60 ARG 0.004 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6497 (mtm110) cc_final: 0.6087 (mtm-85) REVERT: A 24 LYS cc_start: 0.7104 (tttm) cc_final: 0.6886 (mmtm) REVERT: A 342 ARG cc_start: 0.7495 (ttt180) cc_final: 0.6989 (ttp-170) REVERT: A 389 ARG cc_start: 0.7074 (ttm-80) cc_final: 0.6670 (ttm-80) REVERT: B 98 SER cc_start: 0.8417 (m) cc_final: 0.8132 (t) REVERT: B 105 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.8605 (t80) REVERT: N 31 ASN cc_start: 0.7345 (m110) cc_final: 0.7090 (m110) REVERT: N 46 GLU cc_start: 0.7922 (pt0) cc_final: 0.7691 (mt-10) REVERT: R 257 GLU cc_start: 0.6725 (tp30) cc_final: 0.6499 (tt0) REVERT: R 378 LYS cc_start: 0.7731 (ttmt) cc_final: 0.7512 (mtpp) outliers start: 18 outliers final: 17 residues processed: 125 average time/residue: 0.2595 time to fit residues: 41.9512 Evaluate side-chains 126 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 332 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 11 optimal weight: 0.0670 chunk 21 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.159607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.126759 restraints weight = 8404.077| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.89 r_work: 0.3382 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8170 Z= 0.157 Angle : 0.471 6.134 11058 Z= 0.254 Chirality : 0.041 0.136 1224 Planarity : 0.003 0.032 1400 Dihedral : 4.014 19.722 1095 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.32 % Allowed : 15.30 % Favored : 82.39 % 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: 0.17 (0.28), residues: 974 helix: 1.19 (0.28), residues: 371 sheet: -0.67 (0.34), residues: 216 loop : -0.32 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 297 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE A 212 TYR 0.018 0.001 TYR R 157 ARG 0.003 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2260.68 seconds wall clock time: 41 minutes 24.45 seconds (2484.45 seconds total)