Starting phenix.real_space_refine on Mon Mar 11 10:34:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/03_2024/7v9l_31824.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/03_2024/7v9l_31824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/03_2024/7v9l_31824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/03_2024/7v9l_31824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/03_2024/7v9l_31824.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/03_2024/7v9l_31824.pdb" } resolution = 2.6 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= 0.001 sd= 0.022 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 45 5.16 5 C 5108 2.51 5 N 1404 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "R ARG 92": "NH1" <-> "NH2" Residue "R ARG 175": "NH1" <-> "NH2" Residue "R GLU 248": "OE1" <-> "OE2" Residue "R ARG 293": "NH1" <-> "NH2" Residue "R GLU 297": "OE1" <-> "OE2" Residue "R GLU 318": "OE1" <-> "OE2" Residue "Y GLU 22": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8047 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1964 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Chain: "R" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2064 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain breaks: 2 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} 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: "B" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2613 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 4.54, per 1000 atoms: 0.56 Number of scatterers: 8047 At special positions: 0 Unit cell: (97.185, 96.14, 118.085, 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 45 16.00 O 1490 8.00 N 1404 7.00 C 5108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 138 " - pdb=" SG CYS R 208 " 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: 2.89 Conformation dependent library (CDL) restraints added in 1.5 seconds 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1912 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 42.8% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 6 through 39 Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 233 through 241 removed outlier: 4.301A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.864A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (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 312 through 317 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.988A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.658A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 90 Processing helix chain 'R' and resid 91 through 94 Processing helix chain 'R' and resid 95 through 125 Processing helix chain 'R' and resid 134 through 169 removed outlier: 3.679A pdb=" N CYS R 138 " --> pdb=" O SER R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 201 removed outlier: 3.566A pdb=" N PHE R 178 " --> pdb=" O SER R 174 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP R 179 " --> pdb=" O ARG R 175 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP R 180 " --> pdb=" O ARG R 176 " (cutoff:3.500A) Proline residue: R 189 - end of helix Processing helix chain 'R' and resid 214 through 248 removed outlier: 3.714A pdb=" N TRP R 219 " --> pdb=" O SER R 215 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE R 221 " --> pdb=" O TYR R 217 " (cutoff:3.500A) Proline residue: R 224 - end of helix Processing helix chain 'R' and resid 257 through 275 removed outlier: 3.677A pdb=" N TRP R 261 " --> pdb=" O GLN R 257 " (cutoff:3.500A) Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 276 through 282 removed outlier: 3.516A pdb=" N ILE R 280 " --> pdb=" O HIS R 277 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN R 282 " --> pdb=" O ILE R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 298 Proline residue: R 295 - end of helix Processing helix chain 'R' and resid 298 through 313 removed outlier: 3.548A pdb=" N PHE R 303 " --> pdb=" O GLY R 299 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY R 305 " --> pdb=" O GLY R 301 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N PHE R 306 " --> pdb=" O SER R 302 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 327 Processing helix chain 'Y' and resid 7 through 24 Processing helix chain 'Y' and resid 29 through 45 Processing helix chain 'Y' and resid 46 through 48 No H-bonds generated for 'chain 'Y' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.844A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.521A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.436A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.743A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.704A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.575A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.763A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 234 removed outlier: 6.435A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.314A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1176 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: 2.27 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2634 1.34 - 1.46: 1884 1.46 - 1.58: 3640 1.58 - 1.70: 0 1.70 - 1.82: 61 Bond restraints: 8219 Sorted by residual: bond pdb=" CG1 ILE B 43 " pdb=" CD1 ILE B 43 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.92e+00 bond pdb=" C SER R 134 " pdb=" N THR R 135 " ideal model delta sigma weight residual 1.335 1.319 0.016 1.38e-02 5.25e+03 1.39e+00 bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.32e+00 bond pdb=" CB MET B 61 " pdb=" CG MET B 61 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CG ASP B 163 " pdb=" OD1 ASP B 163 " ideal model delta sigma weight residual 1.249 1.229 0.020 1.90e-02 2.77e+03 1.07e+00 ... (remaining 8214 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.74: 123 105.74 - 112.82: 4352 112.82 - 119.89: 2736 119.89 - 126.97: 3818 126.97 - 134.04: 108 Bond angle restraints: 11137 Sorted by residual: angle pdb=" CA TYR R 69 " pdb=" CB TYR R 69 " pdb=" CG TYR R 69 " ideal model delta sigma weight residual 113.90 120.49 -6.59 1.80e+00 3.09e-01 1.34e+01 angle pdb=" CB MET B 61 " pdb=" CG MET B 61 " pdb=" SD MET B 61 " ideal model delta sigma weight residual 112.70 103.94 8.76 3.00e+00 1.11e-01 8.52e+00 angle pdb=" C PHE A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta sigma weight residual 120.38 124.51 -4.13 1.46e+00 4.69e-01 8.00e+00 angle pdb=" CA TRP A 234 " pdb=" CB TRP A 234 " pdb=" CG TRP A 234 " ideal model delta sigma weight residual 113.60 118.80 -5.20 1.90e+00 2.77e-01 7.48e+00 angle pdb=" CA TRP R 155 " pdb=" CB TRP R 155 " pdb=" CG TRP R 155 " ideal model delta sigma weight residual 113.60 108.41 5.19 1.90e+00 2.77e-01 7.46e+00 ... (remaining 11132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4487 17.89 - 35.78: 315 35.78 - 53.67: 42 53.67 - 71.55: 9 71.55 - 89.44: 9 Dihedral angle restraints: 4862 sinusoidal: 1907 harmonic: 2955 Sorted by residual: dihedral pdb=" CA TYR A 253 " pdb=" C TYR A 253 " pdb=" N ARG A 265 " pdb=" CA ARG A 265 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ASP B 163 " pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta harmonic sigma weight residual -180.00 -152.04 -27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA MET B 61 " pdb=" C MET B 61 " pdb=" N HIS B 62 " pdb=" CA HIS B 62 " ideal model delta harmonic sigma weight residual 180.00 152.38 27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 4859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 773 0.039 - 0.078: 342 0.078 - 0.116: 113 0.116 - 0.155: 19 0.155 - 0.194: 5 Chirality restraints: 1252 Sorted by residual: chirality pdb=" CA TRP R 155 " pdb=" N TRP R 155 " pdb=" C TRP R 155 " pdb=" CB TRP R 155 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CA THR A 284 " pdb=" N THR A 284 " pdb=" C THR A 284 " pdb=" CB THR A 284 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CB THR A 210 " pdb=" CA THR A 210 " pdb=" OG1 THR A 210 " pdb=" CG2 THR A 210 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 1249 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 314 " -0.125 9.50e-02 1.11e+02 7.28e-02 2.87e+01 pdb=" NE ARG B 314 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG B 314 " -0.088 2.00e-02 2.50e+03 pdb=" NH1 ARG B 314 " 0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG B 314 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 342 " 0.089 9.50e-02 1.11e+02 5.29e-02 1.61e+01 pdb=" NE ARG A 342 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 342 " 0.066 2.00e-02 2.50e+03 pdb=" NH1 ARG A 342 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 342 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 49 " -0.084 9.50e-02 1.11e+02 4.87e-02 1.29e+01 pdb=" NE ARG B 49 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 49 " -0.059 2.00e-02 2.50e+03 pdb=" NH1 ARG B 49 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG B 49 " 0.017 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 137 2.68 - 3.23: 8196 3.23 - 3.79: 13368 3.79 - 4.34: 18670 4.34 - 4.90: 30293 Nonbonded interactions: 70664 Sorted by model distance: nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.120 2.520 nonbonded pdb=" OH TYR N 117 " pdb=" OD1 ASP B 228 " model vdw 2.191 2.440 nonbonded pdb=" NH1 ARG B 22 " pdb=" O ASP B 258 " model vdw 2.276 2.520 nonbonded pdb=" O PHE R 269 " pdb=" OH TYR R 312 " model vdw 2.295 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.295 2.440 ... (remaining 70659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 2.760 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 24.200 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 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 : 0.004 0.054 8219 Z= 0.284 Angle : 0.691 8.757 11137 Z= 0.409 Chirality : 0.047 0.194 1252 Planarity : 0.007 0.073 1416 Dihedral : 13.080 89.442 2947 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.26), residues: 1003 helix: 0.49 (0.24), residues: 359 sheet: 0.03 (0.35), residues: 207 loop : -0.27 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP R 155 HIS 0.004 0.001 HIS A 357 PHE 0.026 0.002 PHE R 236 TYR 0.034 0.005 TYR R 69 ARG 0.090 0.009 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.6753 (m-30) cc_final: 0.6514 (m-30) REVERT: A 53 LYS cc_start: 0.7122 (pttm) cc_final: 0.6845 (pttp) REVERT: A 209 GLU cc_start: 0.6978 (tt0) cc_final: 0.6730 (tt0) REVERT: A 223 ASP cc_start: 0.7041 (t0) cc_final: 0.6647 (t0) REVERT: A 228 ARG cc_start: 0.7614 (mtp-110) cc_final: 0.7305 (mtp-110) REVERT: A 229 ASP cc_start: 0.7191 (t0) cc_final: 0.6814 (t0) REVERT: A 285 ILE cc_start: 0.8190 (mt) cc_final: 0.7959 (mp) REVERT: A 356 ARG cc_start: 0.6684 (mmm-85) cc_final: 0.6482 (mmm-85) REVERT: A 374 ARG cc_start: 0.6872 (mtt180) cc_final: 0.6584 (mtt-85) REVERT: A 378 ASP cc_start: 0.6555 (p0) cc_final: 0.6235 (p0) REVERT: A 381 ASP cc_start: 0.7418 (t70) cc_final: 0.7068 (t70) REVERT: N 19 ARG cc_start: 0.7379 (ttm170) cc_final: 0.7060 (ttt-90) REVERT: N 31 ASN cc_start: 0.7444 (m110) cc_final: 0.7139 (m110) REVERT: B 27 ASP cc_start: 0.7135 (t0) cc_final: 0.6832 (m-30) REVERT: B 46 ARG cc_start: 0.6951 (mtp180) cc_final: 0.6554 (mtp180) REVERT: B 96 ARG cc_start: 0.6656 (mtm110) cc_final: 0.6182 (mtm110) REVERT: B 101 MET cc_start: 0.8334 (mtp) cc_final: 0.8115 (mtm) REVERT: B 179 THR cc_start: 0.7926 (t) cc_final: 0.7576 (m) REVERT: B 181 THR cc_start: 0.7436 (p) cc_final: 0.6999 (m) REVERT: B 186 ASP cc_start: 0.6956 (m-30) cc_final: 0.6580 (m-30) REVERT: B 197 ARG cc_start: 0.6550 (ttt180) cc_final: 0.6323 (ttt180) REVERT: B 214 ARG cc_start: 0.6737 (mtt180) cc_final: 0.6487 (mtt180) REVERT: B 230 ASN cc_start: 0.8166 (m-40) cc_final: 0.7617 (m110) REVERT: B 246 ASP cc_start: 0.7074 (m-30) cc_final: 0.6469 (m-30) REVERT: B 251 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7774 (mtt180) REVERT: B 254 ASP cc_start: 0.6176 (t70) cc_final: 0.5827 (t70) REVERT: B 258 ASP cc_start: 0.6629 (t0) cc_final: 0.6353 (m-30) REVERT: B 268 ASN cc_start: 0.7541 (m-40) cc_final: 0.7304 (m-40) REVERT: B 295 ASN cc_start: 0.8461 (m-40) cc_final: 0.8241 (m-40) REVERT: B 314 ARG cc_start: 0.7673 (ttt180) cc_final: 0.7220 (ttm170) REVERT: B 322 ASP cc_start: 0.7603 (m-30) cc_final: 0.7337 (m-30) outliers start: 0 outliers final: 1 residues processed: 202 average time/residue: 1.1896 time to fit residues: 254.3207 Evaluate side-chains 176 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 191 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 271 ASN B 125 ASN B 155 ASN B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8219 Z= 0.258 Angle : 0.577 5.871 11137 Z= 0.313 Chirality : 0.043 0.152 1252 Planarity : 0.004 0.041 1416 Dihedral : 5.392 25.616 1109 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.07 % Allowed : 8.96 % Favored : 88.98 % 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 (0.26), residues: 1003 helix: 1.73 (0.25), residues: 367 sheet: 0.10 (0.34), residues: 202 loop : 0.08 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 155 HIS 0.004 0.001 HIS A 357 PHE 0.022 0.002 PHE R 306 TYR 0.030 0.002 TYR R 69 ARG 0.007 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 185 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7131 (ttt90) cc_final: 0.6815 (ttt90) REVERT: A 33 ASP cc_start: 0.6794 (m-30) cc_final: 0.6469 (m-30) REVERT: A 36 VAL cc_start: 0.7078 (t) cc_final: 0.6800 (p) REVERT: A 209 GLU cc_start: 0.6928 (tt0) cc_final: 0.6719 (tt0) REVERT: A 223 ASP cc_start: 0.7107 (t0) cc_final: 0.6685 (t0) REVERT: A 228 ARG cc_start: 0.7640 (mtp-110) cc_final: 0.7003 (mtp-110) REVERT: A 229 ASP cc_start: 0.7265 (t0) cc_final: 0.6807 (t0) REVERT: A 231 ARG cc_start: 0.7515 (ptp-170) cc_final: 0.7139 (mtm180) REVERT: A 236 GLN cc_start: 0.7975 (mt0) cc_final: 0.7745 (mt0) REVERT: A 283 ARG cc_start: 0.7218 (ptt180) cc_final: 0.7007 (ptt180) REVERT: A 285 ILE cc_start: 0.8207 (mt) cc_final: 0.7994 (mp) REVERT: A 343 ASP cc_start: 0.6550 (m-30) cc_final: 0.5962 (m-30) REVERT: A 381 ASP cc_start: 0.7321 (t70) cc_final: 0.7024 (t70) REVERT: R 197 VAL cc_start: 0.6619 (t) cc_final: 0.6406 (m) REVERT: N 25 SER cc_start: 0.7505 (t) cc_final: 0.6801 (p) REVERT: N 31 ASN cc_start: 0.7432 (m110) cc_final: 0.7123 (m110) REVERT: B 27 ASP cc_start: 0.7230 (t0) cc_final: 0.6936 (m-30) REVERT: B 46 ARG cc_start: 0.6962 (mtp180) cc_final: 0.6447 (mtp180) REVERT: B 48 ARG cc_start: 0.8151 (mmt180) cc_final: 0.7867 (mmm160) REVERT: B 61 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7380 (ttp) REVERT: B 96 ARG cc_start: 0.6689 (mtm110) cc_final: 0.6295 (mtm110) REVERT: B 101 MET cc_start: 0.8298 (mtp) cc_final: 0.8087 (mtm) REVERT: B 155 ASN cc_start: 0.6928 (t0) cc_final: 0.6653 (t0) REVERT: B 179 THR cc_start: 0.7918 (t) cc_final: 0.7619 (m) REVERT: B 181 THR cc_start: 0.7511 (p) cc_final: 0.7290 (p) REVERT: B 186 ASP cc_start: 0.6713 (m-30) cc_final: 0.6327 (m-30) REVERT: B 191 SER cc_start: 0.8196 (OUTLIER) cc_final: 0.7871 (t) REVERT: B 197 ARG cc_start: 0.6618 (ttt180) cc_final: 0.6350 (ttt180) REVERT: B 237 ASN cc_start: 0.6818 (t0) cc_final: 0.6465 (t0) REVERT: B 239 ASN cc_start: 0.7625 (m110) cc_final: 0.7324 (m-40) REVERT: B 251 ARG cc_start: 0.8125 (mtt90) cc_final: 0.7923 (mtt180) REVERT: B 258 ASP cc_start: 0.6573 (t0) cc_final: 0.6096 (m-30) REVERT: B 268 ASN cc_start: 0.7743 (m-40) cc_final: 0.7502 (m-40) REVERT: B 304 ARG cc_start: 0.8149 (mtm-85) cc_final: 0.7768 (mmm-85) REVERT: B 314 ARG cc_start: 0.7612 (ttt180) cc_final: 0.7397 (ttt180) REVERT: B 322 ASP cc_start: 0.7572 (m-30) cc_final: 0.7245 (m-30) outliers start: 18 outliers final: 8 residues processed: 188 average time/residue: 1.2541 time to fit residues: 249.0641 Evaluate side-chains 188 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 178 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8219 Z= 0.281 Angle : 0.556 5.476 11137 Z= 0.297 Chirality : 0.043 0.148 1252 Planarity : 0.004 0.043 1416 Dihedral : 5.042 25.190 1107 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.53 % Allowed : 10.45 % Favored : 87.03 % 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: 1.04 (0.26), residues: 1003 helix: 2.03 (0.26), residues: 364 sheet: -0.06 (0.33), residues: 203 loop : 0.01 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 155 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.002 PHE A 212 TYR 0.027 0.002 TYR R 69 ARG 0.009 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 188 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7167 (ttt90) cc_final: 0.6845 (ttt90) REVERT: A 33 ASP cc_start: 0.6788 (m-30) cc_final: 0.6521 (m-30) REVERT: A 228 ARG cc_start: 0.7716 (mtp-110) cc_final: 0.7154 (mtp-110) REVERT: A 229 ASP cc_start: 0.7306 (t0) cc_final: 0.6810 (t0) REVERT: A 231 ARG cc_start: 0.7563 (ptp-170) cc_final: 0.7121 (mtm180) REVERT: A 236 GLN cc_start: 0.7993 (mt0) cc_final: 0.7776 (mt0) REVERT: A 285 ILE cc_start: 0.8240 (mt) cc_final: 0.8034 (mp) REVERT: A 343 ASP cc_start: 0.6481 (m-30) cc_final: 0.5804 (m-30) REVERT: A 356 ARG cc_start: 0.6839 (mmm-85) cc_final: 0.6496 (mmm-85) REVERT: A 381 ASP cc_start: 0.7333 (t70) cc_final: 0.7041 (t70) REVERT: R 197 VAL cc_start: 0.6628 (t) cc_final: 0.6421 (m) REVERT: R 231 VAL cc_start: 0.7743 (t) cc_final: 0.7503 (p) REVERT: N 25 SER cc_start: 0.7497 (t) cc_final: 0.6866 (m) REVERT: N 31 ASN cc_start: 0.7493 (m110) cc_final: 0.7180 (m110) REVERT: B 27 ASP cc_start: 0.7232 (t0) cc_final: 0.6936 (m-30) REVERT: B 45 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7850 (mtt) REVERT: B 46 ARG cc_start: 0.6957 (mtp180) cc_final: 0.6474 (mtp180) REVERT: B 48 ARG cc_start: 0.8176 (mmt180) cc_final: 0.7975 (mmm160) REVERT: B 52 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8022 (ptm160) REVERT: B 61 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7456 (ttp) REVERT: B 101 MET cc_start: 0.8367 (mtp) cc_final: 0.8082 (mtm) REVERT: B 155 ASN cc_start: 0.7061 (t0) cc_final: 0.6676 (t0) REVERT: B 173 THR cc_start: 0.7621 (m) cc_final: 0.7353 (t) REVERT: B 179 THR cc_start: 0.7910 (t) cc_final: 0.7612 (m) REVERT: B 181 THR cc_start: 0.7518 (p) cc_final: 0.7288 (p) REVERT: B 186 ASP cc_start: 0.6696 (m-30) cc_final: 0.6469 (m-30) REVERT: B 191 SER cc_start: 0.8128 (OUTLIER) cc_final: 0.7863 (t) REVERT: B 197 ARG cc_start: 0.6684 (ttt180) cc_final: 0.6370 (ttt180) REVERT: B 237 ASN cc_start: 0.6879 (t0) cc_final: 0.6365 (t0) REVERT: B 239 ASN cc_start: 0.7669 (m110) cc_final: 0.7080 (m-40) REVERT: B 268 ASN cc_start: 0.7756 (m-40) cc_final: 0.7544 (m-40) REVERT: B 314 ARG cc_start: 0.7595 (ttt180) cc_final: 0.7348 (ttt180) REVERT: B 322 ASP cc_start: 0.7593 (m-30) cc_final: 0.7269 (m-30) outliers start: 22 outliers final: 11 residues processed: 194 average time/residue: 1.2121 time to fit residues: 249.9723 Evaluate side-chains 200 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8219 Z= 0.254 Angle : 0.535 6.669 11137 Z= 0.285 Chirality : 0.042 0.160 1252 Planarity : 0.004 0.045 1416 Dihedral : 4.806 24.420 1107 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.64 % Allowed : 12.51 % Favored : 84.85 % 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: 1.03 (0.26), residues: 1003 helix: 2.18 (0.26), residues: 364 sheet: -0.22 (0.32), residues: 203 loop : -0.06 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 155 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.002 PHE A 212 TYR 0.023 0.002 TYR R 69 ARG 0.009 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 194 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7163 (ttt90) cc_final: 0.6848 (ttt90) REVERT: A 33 ASP cc_start: 0.6771 (m-30) cc_final: 0.6541 (m-30) REVERT: A 228 ARG cc_start: 0.7656 (mtp-110) cc_final: 0.7145 (mtp-110) REVERT: A 229 ASP cc_start: 0.7324 (t0) cc_final: 0.6817 (t0) REVERT: A 231 ARG cc_start: 0.7510 (ptp-170) cc_final: 0.7071 (mtm180) REVERT: A 252 ASP cc_start: 0.6196 (t0) cc_final: 0.5661 (t0) REVERT: A 280 ARG cc_start: 0.7102 (tmt-80) cc_final: 0.6633 (tmt-80) REVERT: A 285 ILE cc_start: 0.8240 (mt) cc_final: 0.8016 (mp) REVERT: A 300 LYS cc_start: 0.7229 (ttmt) cc_final: 0.6936 (ttmm) REVERT: A 356 ARG cc_start: 0.6866 (mmm-85) cc_final: 0.6500 (mmm-85) REVERT: A 378 ASP cc_start: 0.6075 (p0) cc_final: 0.5626 (p0) REVERT: A 381 ASP cc_start: 0.7331 (t70) cc_final: 0.7056 (t70) REVERT: R 231 VAL cc_start: 0.7740 (t) cc_final: 0.7501 (p) REVERT: N 25 SER cc_start: 0.7486 (t) cc_final: 0.6888 (m) REVERT: N 31 ASN cc_start: 0.7479 (m110) cc_final: 0.7161 (m110) REVERT: N 111 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7924 (p) REVERT: B 27 ASP cc_start: 0.7222 (t0) cc_final: 0.6928 (m-30) REVERT: B 46 ARG cc_start: 0.6962 (mtp180) cc_final: 0.6481 (mtp180) REVERT: B 48 ARG cc_start: 0.8199 (mmt180) cc_final: 0.7951 (mmm160) REVERT: B 52 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8029 (ptm160) REVERT: B 101 MET cc_start: 0.8383 (mtp) cc_final: 0.8072 (mtm) REVERT: B 150 ARG cc_start: 0.8302 (mmt180) cc_final: 0.7892 (mmt180) REVERT: B 155 ASN cc_start: 0.7123 (t0) cc_final: 0.6682 (t0) REVERT: B 173 THR cc_start: 0.7630 (m) cc_final: 0.7348 (t) REVERT: B 175 GLN cc_start: 0.6882 (mm-40) cc_final: 0.6626 (mm-40) REVERT: B 179 THR cc_start: 0.7838 (t) cc_final: 0.7545 (m) REVERT: B 181 THR cc_start: 0.7472 (p) cc_final: 0.7242 (p) REVERT: B 184 THR cc_start: 0.7821 (t) cc_final: 0.7589 (p) REVERT: B 186 ASP cc_start: 0.6642 (OUTLIER) cc_final: 0.6421 (m-30) REVERT: B 191 SER cc_start: 0.8110 (OUTLIER) cc_final: 0.7830 (t) REVERT: B 197 ARG cc_start: 0.6726 (ttt180) cc_final: 0.6423 (ttt180) REVERT: B 237 ASN cc_start: 0.6981 (t0) cc_final: 0.6432 (t0) REVERT: B 239 ASN cc_start: 0.7653 (m110) cc_final: 0.7051 (m-40) REVERT: B 304 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7652 (mmm-85) REVERT: B 314 ARG cc_start: 0.7548 (ttt180) cc_final: 0.7284 (ttt180) REVERT: B 322 ASP cc_start: 0.7596 (m-30) cc_final: 0.7188 (m-30) outliers start: 23 outliers final: 14 residues processed: 201 average time/residue: 1.2982 time to fit residues: 277.4274 Evaluate side-chains 205 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 71 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 30.0000 chunk 85 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 156 GLN B 230 ASN B 268 ASN B 293 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8219 Z= 0.267 Angle : 0.536 9.104 11137 Z= 0.284 Chirality : 0.042 0.149 1252 Planarity : 0.004 0.047 1416 Dihedral : 4.712 23.854 1107 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.10 % Allowed : 13.20 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1003 helix: 2.24 (0.26), residues: 364 sheet: -0.48 (0.31), residues: 207 loop : -0.13 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.002 PHE A 212 TYR 0.020 0.002 TYR R 69 ARG 0.009 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 183 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7168 (ttt90) cc_final: 0.6852 (ttt90) REVERT: A 33 ASP cc_start: 0.6760 (m-30) cc_final: 0.6533 (m-30) REVERT: A 228 ARG cc_start: 0.7694 (mtp-110) cc_final: 0.7156 (mtp-110) REVERT: A 229 ASP cc_start: 0.7327 (t0) cc_final: 0.6816 (t0) REVERT: A 231 ARG cc_start: 0.7534 (ptp-170) cc_final: 0.7050 (mtm180) REVERT: A 252 ASP cc_start: 0.6153 (t0) cc_final: 0.5754 (t0) REVERT: A 280 ARG cc_start: 0.7074 (tmt-80) cc_final: 0.6615 (tmt-80) REVERT: A 285 ILE cc_start: 0.8208 (mt) cc_final: 0.7982 (mp) REVERT: A 299 GLU cc_start: 0.6485 (mt-10) cc_final: 0.6179 (mt-10) REVERT: A 300 LYS cc_start: 0.7204 (ttmt) cc_final: 0.6913 (ttmm) REVERT: A 356 ARG cc_start: 0.6878 (mmm-85) cc_final: 0.6503 (mmm-85) REVERT: A 381 ASP cc_start: 0.7337 (t70) cc_final: 0.7055 (t70) REVERT: R 231 VAL cc_start: 0.7747 (t) cc_final: 0.7510 (p) REVERT: N 25 SER cc_start: 0.7511 (t) cc_final: 0.6921 (m) REVERT: N 31 ASN cc_start: 0.7493 (m110) cc_final: 0.7152 (m110) REVERT: N 111 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7958 (p) REVERT: B 27 ASP cc_start: 0.7206 (t0) cc_final: 0.6924 (m-30) REVERT: B 45 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7816 (mtt) REVERT: B 46 ARG cc_start: 0.6960 (mtp180) cc_final: 0.6476 (mtp180) REVERT: B 48 ARG cc_start: 0.8236 (mmt180) cc_final: 0.7894 (mmm160) REVERT: B 52 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7949 (ptm160) REVERT: B 101 MET cc_start: 0.8399 (mtp) cc_final: 0.8092 (mtm) REVERT: B 150 ARG cc_start: 0.8312 (mmt180) cc_final: 0.7905 (mmt180) REVERT: B 155 ASN cc_start: 0.7144 (t0) cc_final: 0.6664 (t0) REVERT: B 173 THR cc_start: 0.7644 (m) cc_final: 0.7361 (t) REVERT: B 175 GLN cc_start: 0.6909 (mm-40) cc_final: 0.6650 (mm-40) REVERT: B 179 THR cc_start: 0.7839 (t) cc_final: 0.7548 (m) REVERT: B 181 THR cc_start: 0.7464 (p) cc_final: 0.7230 (p) REVERT: B 184 THR cc_start: 0.7788 (t) cc_final: 0.7573 (p) REVERT: B 186 ASP cc_start: 0.6670 (OUTLIER) cc_final: 0.6385 (m-30) REVERT: B 191 SER cc_start: 0.8114 (OUTLIER) cc_final: 0.7814 (t) REVERT: B 197 ARG cc_start: 0.6809 (ttt180) cc_final: 0.6437 (ttt180) REVERT: B 237 ASN cc_start: 0.7018 (t0) cc_final: 0.6472 (t0) REVERT: B 239 ASN cc_start: 0.7655 (m110) cc_final: 0.7022 (m-40) REVERT: B 304 ARG cc_start: 0.7916 (mtm-85) cc_final: 0.7704 (mmm-85) REVERT: B 314 ARG cc_start: 0.7528 (ttt180) cc_final: 0.7259 (ttt180) REVERT: B 322 ASP cc_start: 0.7600 (m-30) cc_final: 0.7129 (m-30) outliers start: 27 outliers final: 12 residues processed: 196 average time/residue: 1.1982 time to fit residues: 248.6527 Evaluate side-chains 203 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8219 Z= 0.229 Angle : 0.522 7.187 11137 Z= 0.276 Chirality : 0.041 0.147 1252 Planarity : 0.004 0.047 1416 Dihedral : 4.595 23.087 1107 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.41 % Allowed : 14.24 % Favored : 83.35 % 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: 0.91 (0.27), residues: 1003 helix: 2.33 (0.26), residues: 365 sheet: -0.62 (0.32), residues: 208 loop : -0.21 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.019 0.001 PHE A 212 TYR 0.018 0.002 TYR R 69 ARG 0.009 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7163 (ttt90) cc_final: 0.6845 (ttt90) REVERT: A 228 ARG cc_start: 0.7636 (mtp-110) cc_final: 0.7109 (mtp-110) REVERT: A 229 ASP cc_start: 0.7332 (t0) cc_final: 0.6728 (t0) REVERT: A 230 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6997 (mt-10) REVERT: A 231 ARG cc_start: 0.7532 (ptp-170) cc_final: 0.7035 (mtm180) REVERT: A 252 ASP cc_start: 0.6161 (t0) cc_final: 0.5790 (t0) REVERT: A 280 ARG cc_start: 0.7077 (tmt-80) cc_final: 0.6534 (tmt-80) REVERT: A 285 ILE cc_start: 0.8210 (mt) cc_final: 0.7980 (mp) REVERT: A 299 GLU cc_start: 0.6497 (mt-10) cc_final: 0.6187 (mt-10) REVERT: A 300 LYS cc_start: 0.7127 (ttmt) cc_final: 0.6846 (ttmm) REVERT: A 356 ARG cc_start: 0.6881 (mmm-85) cc_final: 0.6499 (mmm-85) REVERT: A 381 ASP cc_start: 0.7336 (t70) cc_final: 0.7048 (t70) REVERT: N 25 SER cc_start: 0.7515 (t) cc_final: 0.6939 (m) REVERT: N 31 ASN cc_start: 0.7487 (m110) cc_final: 0.7136 (m110) REVERT: N 111 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7951 (p) REVERT: B 27 ASP cc_start: 0.7198 (t0) cc_final: 0.6926 (m-30) REVERT: B 45 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7828 (mtt) REVERT: B 46 ARG cc_start: 0.6954 (mtp180) cc_final: 0.6480 (mtp180) REVERT: B 48 ARG cc_start: 0.8219 (mmt180) cc_final: 0.7876 (mmm160) REVERT: B 52 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7882 (ptm160) REVERT: B 101 MET cc_start: 0.8385 (mtp) cc_final: 0.8073 (mtm) REVERT: B 150 ARG cc_start: 0.8323 (mmt180) cc_final: 0.7961 (mmt180) REVERT: B 155 ASN cc_start: 0.7152 (t0) cc_final: 0.6645 (t0) REVERT: B 173 THR cc_start: 0.7630 (m) cc_final: 0.7361 (t) REVERT: B 175 GLN cc_start: 0.6922 (mm-40) cc_final: 0.6674 (mm-40) REVERT: B 179 THR cc_start: 0.7827 (t) cc_final: 0.7537 (m) REVERT: B 181 THR cc_start: 0.7427 (p) cc_final: 0.7191 (p) REVERT: B 184 THR cc_start: 0.7809 (t) cc_final: 0.7584 (p) REVERT: B 186 ASP cc_start: 0.6657 (OUTLIER) cc_final: 0.6312 (m-30) REVERT: B 191 SER cc_start: 0.8088 (OUTLIER) cc_final: 0.7801 (t) REVERT: B 197 ARG cc_start: 0.6865 (ttt180) cc_final: 0.6461 (ttt180) REVERT: B 237 ASN cc_start: 0.7020 (t0) cc_final: 0.6473 (t0) REVERT: B 239 ASN cc_start: 0.7642 (m110) cc_final: 0.6996 (m-40) REVERT: B 314 ARG cc_start: 0.7507 (ttt180) cc_final: 0.7306 (ttt180) REVERT: B 322 ASP cc_start: 0.7652 (m-30) cc_final: 0.7092 (m-30) outliers start: 21 outliers final: 11 residues processed: 193 average time/residue: 1.1988 time to fit residues: 244.8452 Evaluate side-chains 192 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN R 98 ASN B 293 ASN B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8219 Z= 0.210 Angle : 0.506 6.470 11137 Z= 0.267 Chirality : 0.041 0.143 1252 Planarity : 0.004 0.047 1416 Dihedral : 4.448 21.862 1107 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.53 % Allowed : 14.70 % Favored : 82.78 % 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: 0.97 (0.27), residues: 1003 helix: 2.46 (0.26), residues: 365 sheet: -0.69 (0.31), residues: 214 loop : -0.17 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.019 0.001 PHE A 212 TYR 0.019 0.001 TYR R 69 ARG 0.008 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7148 (ttt90) cc_final: 0.6829 (ttt90) REVERT: A 223 ASP cc_start: 0.6956 (t0) cc_final: 0.6512 (t0) REVERT: A 228 ARG cc_start: 0.7657 (mtp-110) cc_final: 0.6934 (mtp-110) REVERT: A 229 ASP cc_start: 0.7314 (t0) cc_final: 0.6691 (t0) REVERT: A 230 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7097 (mt-10) REVERT: A 231 ARG cc_start: 0.7529 (ptp-170) cc_final: 0.7005 (mtm180) REVERT: A 252 ASP cc_start: 0.6142 (t0) cc_final: 0.5789 (t0) REVERT: A 280 ARG cc_start: 0.7093 (tmt-80) cc_final: 0.6609 (tmt-80) REVERT: A 299 GLU cc_start: 0.6503 (mt-10) cc_final: 0.6192 (mt-10) REVERT: A 300 LYS cc_start: 0.7120 (ttmt) cc_final: 0.6856 (ttmm) REVERT: A 356 ARG cc_start: 0.6868 (mmm-85) cc_final: 0.6498 (mmm-85) REVERT: A 381 ASP cc_start: 0.7377 (t70) cc_final: 0.7129 (t70) REVERT: N 25 SER cc_start: 0.7470 (t) cc_final: 0.6921 (m) REVERT: N 28 THR cc_start: 0.7111 (p) cc_final: 0.6669 (t) REVERT: N 31 ASN cc_start: 0.7488 (m110) cc_final: 0.6928 (m110) REVERT: N 34 MET cc_start: 0.7829 (mmm) cc_final: 0.7607 (mmm) REVERT: N 111 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7939 (p) REVERT: N 113 THR cc_start: 0.7932 (p) cc_final: 0.7650 (t) REVERT: B 46 ARG cc_start: 0.6953 (mtp180) cc_final: 0.6480 (mtp180) REVERT: B 48 ARG cc_start: 0.8180 (mmt180) cc_final: 0.7848 (mmm160) REVERT: B 101 MET cc_start: 0.8342 (mtp) cc_final: 0.8051 (mtm) REVERT: B 150 ARG cc_start: 0.8332 (mmt180) cc_final: 0.7935 (mmt180) REVERT: B 155 ASN cc_start: 0.7170 (t0) cc_final: 0.6636 (t0) REVERT: B 173 THR cc_start: 0.7636 (m) cc_final: 0.7368 (t) REVERT: B 175 GLN cc_start: 0.6917 (mm-40) cc_final: 0.6644 (mm-40) REVERT: B 181 THR cc_start: 0.7370 (p) cc_final: 0.7153 (p) REVERT: B 186 ASP cc_start: 0.6627 (OUTLIER) cc_final: 0.6228 (m-30) REVERT: B 191 SER cc_start: 0.8048 (p) cc_final: 0.7799 (t) REVERT: B 237 ASN cc_start: 0.7070 (t0) cc_final: 0.6496 (t0) REVERT: B 239 ASN cc_start: 0.7656 (m110) cc_final: 0.6907 (m-40) REVERT: B 254 ASP cc_start: 0.6431 (t70) cc_final: 0.5888 (t70) REVERT: B 314 ARG cc_start: 0.7487 (ttt180) cc_final: 0.7284 (ttt180) REVERT: B 322 ASP cc_start: 0.7581 (m-30) cc_final: 0.7073 (m-30) outliers start: 22 outliers final: 13 residues processed: 206 average time/residue: 1.1640 time to fit residues: 254.0422 Evaluate side-chains 205 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN R 98 ASN B 293 ASN B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8219 Z= 0.238 Angle : 0.526 9.658 11137 Z= 0.274 Chirality : 0.041 0.140 1252 Planarity : 0.004 0.048 1416 Dihedral : 4.467 21.594 1107 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.18 % Allowed : 16.42 % Favored : 81.40 % 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: 0.92 (0.27), residues: 1003 helix: 2.38 (0.26), residues: 366 sheet: -0.69 (0.32), residues: 214 loop : -0.18 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.020 0.001 PHE A 212 TYR 0.015 0.002 TYR R 69 ARG 0.009 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 190 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7156 (ttt90) cc_final: 0.6842 (ttt90) REVERT: A 223 ASP cc_start: 0.6884 (t0) cc_final: 0.6598 (t0) REVERT: A 229 ASP cc_start: 0.7357 (t0) cc_final: 0.6740 (t0) REVERT: A 230 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6967 (mt-10) REVERT: A 231 ARG cc_start: 0.7543 (ptp-170) cc_final: 0.7061 (mtm180) REVERT: A 252 ASP cc_start: 0.6141 (t0) cc_final: 0.5786 (t0) REVERT: A 280 ARG cc_start: 0.7148 (tmt-80) cc_final: 0.6646 (tmt-80) REVERT: A 299 GLU cc_start: 0.6504 (mt-10) cc_final: 0.6178 (mt-10) REVERT: A 300 LYS cc_start: 0.7115 (ttmt) cc_final: 0.6848 (ttmm) REVERT: A 356 ARG cc_start: 0.6887 (mmm-85) cc_final: 0.6500 (mmm-85) REVERT: A 381 ASP cc_start: 0.7363 (t70) cc_final: 0.7120 (t70) REVERT: R 117 LEU cc_start: 0.7986 (tt) cc_final: 0.7781 (tp) REVERT: N 25 SER cc_start: 0.7492 (t) cc_final: 0.6939 (m) REVERT: N 28 THR cc_start: 0.7144 (p) cc_final: 0.6656 (t) REVERT: N 31 ASN cc_start: 0.7488 (m110) cc_final: 0.6923 (m110) REVERT: N 76 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7548 (ttmm) REVERT: N 111 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7933 (p) REVERT: N 113 THR cc_start: 0.7928 (p) cc_final: 0.7661 (t) REVERT: B 46 ARG cc_start: 0.6963 (mtp180) cc_final: 0.6427 (mtp180) REVERT: B 48 ARG cc_start: 0.8193 (mmt180) cc_final: 0.7888 (mmm160) REVERT: B 101 MET cc_start: 0.8344 (mtp) cc_final: 0.8067 (mtm) REVERT: B 150 ARG cc_start: 0.8332 (mmt180) cc_final: 0.7925 (mmt180) REVERT: B 155 ASN cc_start: 0.7161 (t0) cc_final: 0.6630 (t0) REVERT: B 173 THR cc_start: 0.7636 (m) cc_final: 0.7364 (t) REVERT: B 175 GLN cc_start: 0.6908 (mm-40) cc_final: 0.6629 (mm-40) REVERT: B 179 THR cc_start: 0.7816 (t) cc_final: 0.7527 (m) REVERT: B 181 THR cc_start: 0.7367 (p) cc_final: 0.7141 (p) REVERT: B 186 ASP cc_start: 0.6625 (OUTLIER) cc_final: 0.6376 (m-30) REVERT: B 191 SER cc_start: 0.8032 (p) cc_final: 0.7805 (t) REVERT: B 237 ASN cc_start: 0.7077 (t0) cc_final: 0.6517 (t0) REVERT: B 239 ASN cc_start: 0.7666 (m110) cc_final: 0.6958 (m-40) REVERT: B 322 ASP cc_start: 0.7583 (m-30) cc_final: 0.7083 (m-30) outliers start: 19 outliers final: 11 residues processed: 200 average time/residue: 1.1806 time to fit residues: 250.3248 Evaluate side-chains 205 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN R 98 ASN ** Y 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8219 Z= 0.321 Angle : 0.555 8.538 11137 Z= 0.290 Chirality : 0.042 0.141 1252 Planarity : 0.004 0.049 1416 Dihedral : 4.617 22.038 1107 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.18 % Allowed : 16.65 % Favored : 81.17 % 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 (0.27), residues: 1003 helix: 2.32 (0.26), residues: 361 sheet: -0.73 (0.32), residues: 214 loop : -0.23 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.022 0.002 PHE A 212 TYR 0.017 0.002 TYR N 95 ARG 0.010 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7182 (ttt90) cc_final: 0.6870 (ttt90) REVERT: A 229 ASP cc_start: 0.7365 (t0) cc_final: 0.6757 (t0) REVERT: A 230 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7042 (mt-10) REVERT: A 231 ARG cc_start: 0.7550 (ptp-170) cc_final: 0.7075 (mtm180) REVERT: A 252 ASP cc_start: 0.6140 (t0) cc_final: 0.5794 (t0) REVERT: A 280 ARG cc_start: 0.7122 (tmt-80) cc_final: 0.6618 (tmt-80) REVERT: A 285 ILE cc_start: 0.8184 (mt) cc_final: 0.7905 (mp) REVERT: A 299 GLU cc_start: 0.6504 (mt-10) cc_final: 0.6189 (mt-10) REVERT: A 300 LYS cc_start: 0.7140 (ttmt) cc_final: 0.6841 (ttmm) REVERT: A 356 ARG cc_start: 0.6873 (mmm-85) cc_final: 0.6511 (mmm-85) REVERT: A 381 ASP cc_start: 0.7388 (t70) cc_final: 0.7125 (t70) REVERT: R 117 LEU cc_start: 0.8008 (tt) cc_final: 0.7805 (tp) REVERT: N 25 SER cc_start: 0.7490 (t) cc_final: 0.6789 (p) REVERT: N 31 ASN cc_start: 0.7433 (m110) cc_final: 0.7021 (m110) REVERT: N 76 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7575 (ttmm) REVERT: N 113 THR cc_start: 0.7928 (p) cc_final: 0.7683 (t) REVERT: B 46 ARG cc_start: 0.6973 (mtp180) cc_final: 0.6453 (mtp180) REVERT: B 48 ARG cc_start: 0.8254 (mmt180) cc_final: 0.7937 (mmm160) REVERT: B 101 MET cc_start: 0.8352 (mtp) cc_final: 0.8098 (mtm) REVERT: B 150 ARG cc_start: 0.8320 (mmt180) cc_final: 0.7870 (mmt180) REVERT: B 155 ASN cc_start: 0.7125 (t0) cc_final: 0.6577 (t0) REVERT: B 173 THR cc_start: 0.7630 (m) cc_final: 0.7346 (t) REVERT: B 175 GLN cc_start: 0.6913 (mm-40) cc_final: 0.6665 (mm-40) REVERT: B 179 THR cc_start: 0.7902 (t) cc_final: 0.7603 (m) REVERT: B 181 THR cc_start: 0.7411 (p) cc_final: 0.7172 (p) REVERT: B 186 ASP cc_start: 0.6662 (OUTLIER) cc_final: 0.6413 (m-30) REVERT: B 191 SER cc_start: 0.8012 (p) cc_final: 0.7809 (t) REVERT: B 237 ASN cc_start: 0.7101 (t0) cc_final: 0.6586 (t0) REVERT: B 239 ASN cc_start: 0.7667 (m110) cc_final: 0.7042 (m-40) REVERT: B 322 ASP cc_start: 0.7548 (m-30) cc_final: 0.7057 (m-30) outliers start: 19 outliers final: 13 residues processed: 196 average time/residue: 1.2427 time to fit residues: 257.6466 Evaluate side-chains 201 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 185 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 chunk 90 optimal weight: 0.9990 chunk 78 optimal weight: 0.0170 chunk 8 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN B 293 ASN B 295 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8219 Z= 0.205 Angle : 0.512 8.377 11137 Z= 0.269 Chirality : 0.041 0.140 1252 Planarity : 0.004 0.048 1416 Dihedral : 4.433 20.686 1107 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.41 % Allowed : 16.30 % Favored : 81.29 % 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: 0.81 (0.27), residues: 1003 helix: 2.28 (0.26), residues: 370 sheet: -0.76 (0.32), residues: 214 loop : -0.25 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.019 0.001 PHE A 212 TYR 0.013 0.001 TYR R 69 ARG 0.009 0.000 ARG A 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7143 (ttt90) cc_final: 0.6813 (ttt90) REVERT: A 229 ASP cc_start: 0.7383 (t0) cc_final: 0.6758 (t0) REVERT: A 230 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6880 (mt-10) REVERT: A 231 ARG cc_start: 0.7511 (ptp-170) cc_final: 0.7015 (mtm180) REVERT: A 252 ASP cc_start: 0.6203 (t0) cc_final: 0.5871 (t0) REVERT: A 280 ARG cc_start: 0.7111 (tmt-80) cc_final: 0.6603 (tmt-80) REVERT: A 285 ILE cc_start: 0.8193 (mt) cc_final: 0.7919 (mp) REVERT: A 299 GLU cc_start: 0.6494 (mt-10) cc_final: 0.6187 (mt-10) REVERT: A 300 LYS cc_start: 0.7106 (ttmt) cc_final: 0.6845 (ttmm) REVERT: A 356 ARG cc_start: 0.6860 (mmm-85) cc_final: 0.6498 (mmm-85) REVERT: A 381 ASP cc_start: 0.7343 (t70) cc_final: 0.7111 (t70) REVERT: R 117 LEU cc_start: 0.7967 (tt) cc_final: 0.7750 (tp) REVERT: N 25 SER cc_start: 0.7485 (t) cc_final: 0.6949 (m) REVERT: N 28 THR cc_start: 0.7443 (m) cc_final: 0.6721 (t) REVERT: N 31 ASN cc_start: 0.7501 (m110) cc_final: 0.7129 (m110) REVERT: N 76 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7555 (ttmm) REVERT: N 113 THR cc_start: 0.7892 (p) cc_final: 0.7619 (t) REVERT: B 48 ARG cc_start: 0.8172 (mmt180) cc_final: 0.7895 (mmm160) REVERT: B 61 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7520 (tmm) REVERT: B 101 MET cc_start: 0.8403 (mtp) cc_final: 0.8102 (mtm) REVERT: B 150 ARG cc_start: 0.8348 (mmt180) cc_final: 0.7896 (mmt180) REVERT: B 155 ASN cc_start: 0.7163 (t0) cc_final: 0.6586 (t0) REVERT: B 173 THR cc_start: 0.7632 (m) cc_final: 0.7353 (t) REVERT: B 175 GLN cc_start: 0.6900 (mm-40) cc_final: 0.6600 (mm-40) REVERT: B 179 THR cc_start: 0.7827 (t) cc_final: 0.7529 (m) REVERT: B 181 THR cc_start: 0.7377 (p) cc_final: 0.7141 (p) REVERT: B 186 ASP cc_start: 0.6589 (OUTLIER) cc_final: 0.6337 (m-30) REVERT: B 191 SER cc_start: 0.8010 (p) cc_final: 0.7795 (t) REVERT: B 237 ASN cc_start: 0.7064 (t0) cc_final: 0.6497 (t0) REVERT: B 239 ASN cc_start: 0.7650 (m110) cc_final: 0.6858 (m-40) REVERT: B 254 ASP cc_start: 0.6506 (t70) cc_final: 0.5922 (t70) REVERT: B 322 ASP cc_start: 0.7586 (m-30) cc_final: 0.7081 (m-30) outliers start: 21 outliers final: 13 residues processed: 196 average time/residue: 1.2041 time to fit residues: 249.7556 Evaluate side-chains 199 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.0060 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.0270 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 0.0980 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN B 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.153284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.133917 restraints weight = 10439.259| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.84 r_work: 0.3656 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8219 Z= 0.182 Angle : 0.506 8.087 11137 Z= 0.265 Chirality : 0.041 0.138 1252 Planarity : 0.004 0.049 1416 Dihedral : 4.320 19.989 1107 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.07 % Allowed : 16.65 % Favored : 81.29 % 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: 0.86 (0.27), residues: 1003 helix: 2.34 (0.26), residues: 371 sheet: -0.74 (0.32), residues: 214 loop : -0.26 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE N 29 TYR 0.013 0.001 TYR R 69 ARG 0.009 0.000 ARG A 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4209.96 seconds wall clock time: 75 minutes 4.00 seconds (4504.00 seconds total)