Starting phenix.real_space_refine on Sat Aug 3 17:09:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoi_38530/08_2024/8xoi_38530.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoi_38530/08_2024/8xoi_38530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoi_38530/08_2024/8xoi_38530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoi_38530/08_2024/8xoi_38530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoi_38530/08_2024/8xoi_38530.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoi_38530/08_2024/8xoi_38530.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 5566 2.51 5 N 1522 2.21 5 O 1609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 268": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "R GLU 218": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8753 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1866 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2554 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1735 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2162 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain breaks: 3 Time building chain proxies: 5.25, per 1000 atoms: 0.60 Number of scatterers: 8753 At special positions: 0 Unit cell: (113.526, 121.023, 109.242, 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 1609 8.00 N 1522 7.00 C 5566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.52 Conformation dependent library (CDL) restraints added in 1.4 seconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 39.6% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 15 through 40 removed outlier: 3.603A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.746A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.540A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.529A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'G' and resid 7 through 25 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 53 through 87 removed outlier: 4.612A pdb=" N PHE R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) Proline residue: R 71 - end of helix removed outlier: 3.518A pdb=" N PHE R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 91 Processing helix chain 'R' and resid 92 through 116 removed outlier: 3.549A pdb=" N LEU R 96 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 124 removed outlier: 4.308A pdb=" N TYR R 123 " --> pdb=" O LEU R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 161 Processing helix chain 'R' and resid 170 through 200 Proline residue: R 192 - end of helix Processing helix chain 'R' and resid 211 through 223 Processing helix chain 'R' and resid 223 through 247 Processing helix chain 'R' and resid 254 through 285 Proline residue: R 274 - end of helix Processing helix chain 'R' and resid 302 through 325 removed outlier: 3.902A pdb=" N SER R 317 " --> pdb=" O ALA R 313 " (cutoff:3.500A) Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 329 through 342 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.418A pdb=" N LEU A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE A 222 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.852A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.576A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.927A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.238A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.910A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.384A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.792A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.545A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.545A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.470A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.174A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1293 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: 2.97 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2357 1.33 - 1.45: 1616 1.45 - 1.57: 4875 1.57 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 8930 Sorted by residual: bond pdb=" CA ASN B 237 " pdb=" C ASN B 237 " ideal model delta sigma weight residual 1.522 1.552 -0.030 1.39e-02 5.18e+03 4.77e+00 bond pdb=" C ASN R 77 " pdb=" O ASN R 77 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.16e-02 7.43e+03 4.14e+00 bond pdb=" N TYR A 391 " pdb=" CA TYR A 391 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.25e-02 6.40e+03 3.68e+00 bond pdb=" N THR G 6 " pdb=" CA THR G 6 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 bond pdb=" N GLU B 3 " pdb=" CA GLU B 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 ... (remaining 8925 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.31: 251 107.31 - 114.00: 5059 114.00 - 120.69: 3577 120.69 - 127.38: 3112 127.38 - 134.07: 93 Bond angle restraints: 12092 Sorted by residual: angle pdb=" N MET E 192 " pdb=" CA MET E 192 " pdb=" CB MET E 192 " ideal model delta sigma weight residual 114.17 109.27 4.90 1.14e+00 7.69e-01 1.85e+01 angle pdb=" N TYR B 105 " pdb=" CA TYR B 105 " pdb=" C TYR B 105 " ideal model delta sigma weight residual 108.76 102.73 6.03 1.69e+00 3.50e-01 1.27e+01 angle pdb=" C SER R 325 " pdb=" N PHE R 326 " pdb=" CA PHE R 326 " ideal model delta sigma weight residual 122.65 117.90 4.75 1.60e+00 3.91e-01 8.80e+00 angle pdb=" CA ASN R 77 " pdb=" C ASN R 77 " pdb=" O ASN R 77 " ideal model delta sigma weight residual 120.70 117.77 2.93 1.03e+00 9.43e-01 8.09e+00 angle pdb=" N ILE A 235 " pdb=" CA ILE A 235 " pdb=" C ILE A 235 " ideal model delta sigma weight residual 112.98 109.45 3.53 1.25e+00 6.40e-01 7.99e+00 ... (remaining 12087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 4680 17.51 - 35.01: 481 35.01 - 52.52: 111 52.52 - 70.03: 19 70.03 - 87.54: 7 Dihedral angle restraints: 5298 sinusoidal: 2063 harmonic: 3235 Sorted by residual: dihedral pdb=" CA PHE R 326 " pdb=" C PHE R 326 " pdb=" N LEU R 327 " pdb=" CA LEU R 327 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP A 378 " pdb=" CB ASP A 378 " pdb=" CG ASP A 378 " pdb=" OD1 ASP A 378 " ideal model delta sinusoidal sigma weight residual -30.00 -89.81 59.81 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 5295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 943 0.033 - 0.067: 304 0.067 - 0.100: 75 0.100 - 0.133: 50 0.133 - 0.166: 5 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CA TYR B 105 " pdb=" N TYR B 105 " pdb=" C TYR B 105 " pdb=" CB TYR B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE E 189 " pdb=" N ILE E 189 " pdb=" C ILE E 189 " pdb=" CB ILE E 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA TYR A 391 " pdb=" N TYR A 391 " pdb=" C TYR A 391 " pdb=" CB TYR A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 1374 not shown) Planarity restraints: 1534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO A 321 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 236 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C PRO B 236 " -0.033 2.00e-02 2.50e+03 pdb=" O PRO B 236 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN B 237 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 233 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C CYS B 233 " -0.029 2.00e-02 2.50e+03 pdb=" O CYS B 233 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE B 234 " 0.010 2.00e-02 2.50e+03 ... (remaining 1531 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1062 2.75 - 3.29: 8908 3.29 - 3.82: 14943 3.82 - 4.36: 17970 4.36 - 4.90: 31189 Nonbonded interactions: 74072 Sorted by model distance: nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.211 3.040 nonbonded pdb=" OE2 GLU A 21 " pdb=" OG SER E 52 " model vdw 2.226 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.271 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD2 ASP B 76 " model vdw 2.290 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.309 3.040 ... (remaining 74067 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.200 Find NCS groups from input model: 0.120 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.003 0.034 8930 Z= 0.194 Angle : 0.539 6.030 12092 Z= 0.315 Chirality : 0.040 0.166 1377 Planarity : 0.004 0.053 1534 Dihedral : 15.215 87.536 3202 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.32 % Allowed : 13.19 % Favored : 86.50 % 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: 0.82 (0.26), residues: 1091 helix: 2.06 (0.25), residues: 417 sheet: -0.54 (0.31), residues: 262 loop : -0.20 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS B 91 PHE 0.014 0.001 PHE R 326 TYR 0.011 0.001 TYR E 103 ARG 0.009 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 160 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.7991 (ttp) cc_final: 0.7719 (tmm) REVERT: B 212 ASP cc_start: 0.7801 (t70) cc_final: 0.7341 (t70) REVERT: B 217 MET cc_start: 0.7918 (ppp) cc_final: 0.7660 (ppp) REVERT: B 337 LYS cc_start: 0.9066 (mttm) cc_final: 0.8783 (mttm) REVERT: G 20 LYS cc_start: 0.8050 (ttmt) cc_final: 0.7363 (ptmt) REVERT: R 64 LEU cc_start: 0.7654 (tp) cc_final: 0.7434 (mt) REVERT: R 314 PHE cc_start: 0.7976 (m-80) cc_final: 0.7551 (m-80) outliers start: 3 outliers final: 3 residues processed: 162 average time/residue: 0.2362 time to fit residues: 50.6739 Evaluate side-chains 140 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain R residue 99 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.0050 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 227 GLN B 259 GLN R 200 HIS R 282 HIS R 341 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8930 Z= 0.233 Angle : 0.557 8.161 12092 Z= 0.298 Chirality : 0.042 0.147 1377 Planarity : 0.004 0.039 1534 Dihedral : 5.078 59.524 1213 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.43 % Allowed : 13.71 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1091 helix: 2.23 (0.25), residues: 409 sheet: -0.38 (0.32), residues: 252 loop : -0.18 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.004 0.001 HIS R 200 PHE 0.016 0.002 PHE R 326 TYR 0.010 0.001 TYR E 190 ARG 0.005 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.4446 (OUTLIER) cc_final: 0.4185 (pt0) REVERT: B 212 ASP cc_start: 0.7820 (t70) cc_final: 0.7607 (t70) REVERT: B 337 LYS cc_start: 0.9139 (mttm) cc_final: 0.8871 (mttm) REVERT: E 160 ARG cc_start: 0.7397 (mtm-85) cc_final: 0.6637 (mtp85) outliers start: 23 outliers final: 10 residues processed: 179 average time/residue: 0.2323 time to fit residues: 55.7587 Evaluate side-chains 152 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 141 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 197 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN E 179 GLN R 54 GLN ** R 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 200 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8930 Z= 0.164 Angle : 0.497 5.792 12092 Z= 0.266 Chirality : 0.041 0.144 1377 Planarity : 0.003 0.030 1534 Dihedral : 4.842 59.800 1211 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.22 % Allowed : 14.66 % Favored : 83.12 % 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: 1.05 (0.25), residues: 1091 helix: 2.42 (0.25), residues: 407 sheet: -0.41 (0.30), residues: 271 loop : -0.20 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS R 245 PHE 0.016 0.001 PHE R 269 TYR 0.008 0.001 TYR E 59 ARG 0.005 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.4174 (OUTLIER) cc_final: 0.3946 (pt0) REVERT: E 59 TYR cc_start: 0.8075 (m-80) cc_final: 0.7770 (m-80) REVERT: E 160 ARG cc_start: 0.7332 (mtm-85) cc_final: 0.6642 (mtp85) REVERT: E 192 MET cc_start: 0.8540 (ttp) cc_final: 0.8277 (tmm) REVERT: R 54 GLN cc_start: 0.6583 (OUTLIER) cc_final: 0.6362 (mp10) REVERT: R 77 ASN cc_start: 0.8250 (m110) cc_final: 0.7751 (m110) REVERT: R 183 MET cc_start: 0.6870 (ttt) cc_final: 0.6323 (tpp) outliers start: 21 outliers final: 14 residues processed: 169 average time/residue: 0.2140 time to fit residues: 49.1866 Evaluate side-chains 155 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 54 GLN Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 197 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 0.2980 chunk 104 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** R 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 245 HIS R 247 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8930 Z= 0.271 Angle : 0.534 7.176 12092 Z= 0.285 Chirality : 0.042 0.148 1377 Planarity : 0.004 0.031 1534 Dihedral : 5.029 59.610 1211 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.06 % Allowed : 15.30 % Favored : 81.65 % 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: 0.93 (0.25), residues: 1091 helix: 2.22 (0.25), residues: 413 sheet: -0.35 (0.31), residues: 253 loop : -0.31 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.008 0.001 HIS R 245 PHE 0.019 0.002 PHE R 326 TYR 0.013 0.002 TYR R 156 ARG 0.006 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6540 (tm-30) REVERT: B 3 GLU cc_start: 0.4458 (OUTLIER) cc_final: 0.4148 (pt0) REVERT: B 217 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7695 (ppp) REVERT: E 59 TYR cc_start: 0.8120 (m-80) cc_final: 0.7796 (m-80) REVERT: E 160 ARG cc_start: 0.7297 (mtm-85) cc_final: 0.6675 (mtp85) REVERT: E 192 MET cc_start: 0.8489 (ttp) cc_final: 0.8210 (tmm) REVERT: R 77 ASN cc_start: 0.8275 (m110) cc_final: 0.8027 (m-40) REVERT: R 183 MET cc_start: 0.6847 (ttt) cc_final: 0.6221 (tpp) REVERT: R 190 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7227 (mp) REVERT: R 283 LEU cc_start: 0.7823 (mt) cc_final: 0.7613 (mt) outliers start: 29 outliers final: 19 residues processed: 156 average time/residue: 0.2362 time to fit residues: 50.2254 Evaluate side-chains 156 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 197 HIS Chi-restraints excluded: chain R residue 220 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN R 54 GLN R 77 ASN R 247 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8930 Z= 0.187 Angle : 0.486 5.981 12092 Z= 0.259 Chirality : 0.040 0.139 1377 Planarity : 0.003 0.032 1534 Dihedral : 4.711 59.628 1211 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.95 % Allowed : 15.61 % Favored : 81.43 % 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: 1.10 (0.25), residues: 1091 helix: 2.48 (0.25), residues: 407 sheet: -0.25 (0.31), residues: 248 loop : -0.32 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS G 44 PHE 0.013 0.001 PHE R 326 TYR 0.009 0.001 TYR E 190 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8139 (tt0) cc_final: 0.7915 (tt0) REVERT: A 213 GLN cc_start: 0.7818 (tt0) cc_final: 0.7434 (tt0) REVERT: A 230 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6541 (tm-30) REVERT: B 3 GLU cc_start: 0.4526 (OUTLIER) cc_final: 0.4216 (pt0) REVERT: B 217 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7760 (ppp) REVERT: B 266 HIS cc_start: 0.7056 (OUTLIER) cc_final: 0.6666 (t-170) REVERT: E 59 TYR cc_start: 0.8099 (m-80) cc_final: 0.7779 (m-80) REVERT: E 160 ARG cc_start: 0.7249 (mtm-85) cc_final: 0.6654 (mtp85) REVERT: E 192 MET cc_start: 0.8484 (ttp) cc_final: 0.8257 (tmm) REVERT: R 54 GLN cc_start: 0.6517 (OUTLIER) cc_final: 0.6255 (mp10) REVERT: R 77 ASN cc_start: 0.8310 (m-40) cc_final: 0.7998 (m-40) REVERT: R 183 MET cc_start: 0.6883 (ttt) cc_final: 0.6262 (tpp) outliers start: 28 outliers final: 14 residues processed: 164 average time/residue: 0.2190 time to fit residues: 49.2278 Evaluate side-chains 152 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain R residue 54 GLN Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 197 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 86 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN R 247 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8930 Z= 0.144 Angle : 0.483 8.459 12092 Z= 0.255 Chirality : 0.039 0.135 1377 Planarity : 0.003 0.033 1534 Dihedral : 4.444 59.839 1211 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.32 % Allowed : 15.61 % Favored : 82.07 % 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: 1.23 (0.26), residues: 1091 helix: 2.61 (0.25), residues: 407 sheet: -0.14 (0.31), residues: 254 loop : -0.28 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS R 247 PHE 0.014 0.001 PHE R 70 TYR 0.008 0.001 TYR E 190 ARG 0.005 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8120 (tt0) cc_final: 0.7916 (tt0) REVERT: A 213 GLN cc_start: 0.7854 (tt0) cc_final: 0.7472 (tt0) REVERT: A 230 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6403 (tm-30) REVERT: B 3 GLU cc_start: 0.4501 (OUTLIER) cc_final: 0.4216 (pt0) REVERT: B 217 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7781 (ppp) REVERT: B 266 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.6673 (t-170) REVERT: E 59 TYR cc_start: 0.8085 (m-80) cc_final: 0.7785 (m-80) REVERT: E 160 ARG cc_start: 0.7176 (mtm-85) cc_final: 0.6625 (mtp85) REVERT: E 192 MET cc_start: 0.8463 (ttp) cc_final: 0.8248 (tmm) REVERT: R 64 LEU cc_start: 0.8072 (tt) cc_final: 0.7828 (mt) REVERT: R 77 ASN cc_start: 0.8399 (m-40) cc_final: 0.7934 (m110) REVERT: R 183 MET cc_start: 0.6841 (ttt) cc_final: 0.6307 (tpp) REVERT: R 269 PHE cc_start: 0.8151 (t80) cc_final: 0.7817 (t80) outliers start: 22 outliers final: 13 residues processed: 161 average time/residue: 0.2240 time to fit residues: 48.9856 Evaluate side-chains 150 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 197 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN E 142 GLN E 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8930 Z= 0.283 Angle : 0.538 7.349 12092 Z= 0.284 Chirality : 0.041 0.147 1377 Planarity : 0.004 0.035 1534 Dihedral : 4.655 59.966 1210 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.38 % Allowed : 15.19 % Favored : 81.43 % 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: 0.99 (0.25), residues: 1091 helix: 2.32 (0.25), residues: 413 sheet: -0.25 (0.31), residues: 254 loop : -0.36 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.021 0.002 PHE R 326 TYR 0.015 0.002 TYR R 156 ARG 0.004 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6530 (tm-30) REVERT: B 3 GLU cc_start: 0.4629 (OUTLIER) cc_final: 0.4304 (pt0) REVERT: B 217 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7734 (ppp) REVERT: B 266 HIS cc_start: 0.7222 (OUTLIER) cc_final: 0.6749 (t-170) REVERT: E 59 TYR cc_start: 0.8118 (m-80) cc_final: 0.7811 (m-80) REVERT: E 160 ARG cc_start: 0.7198 (mtm-85) cc_final: 0.6632 (mtp85) REVERT: E 192 MET cc_start: 0.8495 (ttp) cc_final: 0.8253 (tmm) REVERT: R 64 LEU cc_start: 0.8133 (tt) cc_final: 0.7820 (mt) REVERT: R 183 MET cc_start: 0.6777 (ttt) cc_final: 0.6237 (tpp) REVERT: R 315 SER cc_start: 0.8893 (m) cc_final: 0.8644 (p) outliers start: 32 outliers final: 19 residues processed: 163 average time/residue: 0.2164 time to fit residues: 48.5401 Evaluate side-chains 157 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 197 HIS Chi-restraints excluded: chain R residue 220 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8930 Z= 0.224 Angle : 0.518 7.440 12092 Z= 0.273 Chirality : 0.041 0.143 1377 Planarity : 0.003 0.037 1534 Dihedral : 4.592 59.780 1210 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.85 % Allowed : 16.35 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1091 helix: 2.34 (0.25), residues: 413 sheet: -0.17 (0.31), residues: 248 loop : -0.41 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS G 44 PHE 0.018 0.001 PHE R 314 TYR 0.011 0.001 TYR E 190 ARG 0.005 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 137 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.7849 (tt0) cc_final: 0.7468 (tt0) REVERT: A 230 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6525 (tm-30) REVERT: A 265 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7196 (ptm-80) REVERT: B 3 GLU cc_start: 0.4642 (OUTLIER) cc_final: 0.4307 (pt0) REVERT: B 195 ASP cc_start: 0.7957 (p0) cc_final: 0.7655 (p0) REVERT: B 217 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7749 (ppp) REVERT: B 266 HIS cc_start: 0.7165 (OUTLIER) cc_final: 0.6744 (t-170) REVERT: E 59 TYR cc_start: 0.8114 (m-80) cc_final: 0.7810 (m-80) REVERT: E 160 ARG cc_start: 0.7190 (mtm-85) cc_final: 0.6627 (mtp85) REVERT: E 180 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7542 (mtt90) REVERT: E 192 MET cc_start: 0.8454 (ttp) cc_final: 0.8224 (tmm) REVERT: R 77 ASN cc_start: 0.8492 (m-40) cc_final: 0.8149 (m-40) REVERT: R 183 MET cc_start: 0.6768 (ttt) cc_final: 0.6223 (tpp) outliers start: 27 outliers final: 17 residues processed: 157 average time/residue: 0.2200 time to fit residues: 46.7372 Evaluate side-chains 155 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 197 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN R 247 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8930 Z= 0.161 Angle : 0.479 6.937 12092 Z= 0.256 Chirality : 0.040 0.137 1377 Planarity : 0.003 0.037 1534 Dihedral : 4.412 59.952 1210 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.16 % Allowed : 15.93 % Favored : 80.91 % 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: 1.21 (0.25), residues: 1091 helix: 2.54 (0.25), residues: 406 sheet: -0.08 (0.31), residues: 247 loop : -0.29 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS G 44 PHE 0.012 0.001 PHE R 326 TYR 0.008 0.001 TYR E 103 ARG 0.005 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 140 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.7830 (tt0) cc_final: 0.7459 (tt0) REVERT: A 230 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6443 (tm-30) REVERT: B 3 GLU cc_start: 0.4618 (OUTLIER) cc_final: 0.4317 (pt0) REVERT: B 195 ASP cc_start: 0.7803 (p0) cc_final: 0.7485 (p0) REVERT: B 217 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7717 (ppp) REVERT: E 59 TYR cc_start: 0.8114 (m-80) cc_final: 0.7826 (m-80) REVERT: E 160 ARG cc_start: 0.7192 (mtm-85) cc_final: 0.6621 (mtp85) REVERT: E 180 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7595 (mtt90) REVERT: R 77 ASN cc_start: 0.8383 (m-40) cc_final: 0.8055 (m-40) REVERT: R 183 MET cc_start: 0.6756 (ttt) cc_final: 0.6204 (tpp) outliers start: 30 outliers final: 19 residues processed: 162 average time/residue: 0.2110 time to fit residues: 46.3155 Evaluate side-chains 159 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 197 HIS Chi-restraints excluded: chain R residue 247 HIS Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 326 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 247 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8930 Z= 0.202 Angle : 0.508 8.175 12092 Z= 0.267 Chirality : 0.040 0.140 1377 Planarity : 0.003 0.037 1534 Dihedral : 4.464 59.854 1210 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.53 % Allowed : 16.56 % Favored : 80.91 % 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: 1.19 (0.25), residues: 1091 helix: 2.50 (0.25), residues: 406 sheet: -0.03 (0.31), residues: 247 loop : -0.32 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS G 44 PHE 0.014 0.001 PHE R 70 TYR 0.011 0.001 TYR E 190 ARG 0.005 0.000 ARG E 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.7896 (tt0) cc_final: 0.7523 (tt0) REVERT: A 230 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6445 (tm-30) REVERT: B 3 GLU cc_start: 0.4648 (OUTLIER) cc_final: 0.4337 (pt0) REVERT: B 195 ASP cc_start: 0.7834 (p0) cc_final: 0.7537 (p0) REVERT: B 217 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7724 (ppp) REVERT: B 266 HIS cc_start: 0.7260 (OUTLIER) cc_final: 0.6841 (t-170) REVERT: E 59 TYR cc_start: 0.8124 (m-80) cc_final: 0.7805 (m-80) REVERT: E 160 ARG cc_start: 0.7215 (mtm-85) cc_final: 0.6611 (mtp85) REVERT: E 180 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7619 (mtt90) REVERT: R 77 ASN cc_start: 0.8371 (m-40) cc_final: 0.8039 (m-40) REVERT: R 183 MET cc_start: 0.6753 (ttt) cc_final: 0.6203 (tpp) outliers start: 24 outliers final: 19 residues processed: 160 average time/residue: 0.2159 time to fit residues: 47.0660 Evaluate side-chains 164 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 197 HIS Chi-restraints excluded: chain R residue 247 HIS Chi-restraints excluded: chain R residue 260 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 88 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 75 optimal weight: 0.3980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 247 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.162891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124076 restraints weight = 10616.332| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.69 r_work: 0.3007 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8930 Z= 0.189 Angle : 0.505 8.158 12092 Z= 0.266 Chirality : 0.040 0.139 1377 Planarity : 0.003 0.039 1534 Dihedral : 4.450 59.788 1210 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.85 % Allowed : 16.56 % Favored : 80.59 % 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: 1.19 (0.25), residues: 1091 helix: 2.51 (0.25), residues: 406 sheet: -0.03 (0.31), residues: 247 loop : -0.32 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS R 247 PHE 0.013 0.001 PHE R 70 TYR 0.010 0.001 TYR E 190 ARG 0.005 0.000 ARG E 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2129.31 seconds wall clock time: 38 minutes 45.30 seconds (2325.30 seconds total)