Starting phenix.real_space_refine (version: dev) on Sun Dec 11 23:05:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/12_2022/7v9l_31824.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/12_2022/7v9l_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_31824/12_2022/7v9l_31824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/12_2022/7v9l_31824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/12_2022/7v9l_31824.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/12_2022/7v9l_31824.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 5.00, per 1000 atoms: 0.62 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: 3.48 Conformation dependent library (CDL) restraints added in 1.2 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: 0.45 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: 2.42 Time building geometry restraints manager: 3.65 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 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. 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.920 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.090 Process input model: 25.230 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 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 : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 0.952 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 202 average time/residue: 1.0647 time to fit residues: 229.1096 Evaluate side-chains 175 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1218 time to fit residues: 1.4233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 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: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 271 ASN B 125 ASN B 155 ASN B 230 ASN B 239 ASN B 268 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.1505 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= 0.267 Angle : 0.587 5.836 11137 Z= 0.318 Chirality : 0.043 0.151 1252 Planarity : 0.004 0.042 1416 Dihedral : 5.377 25.580 1107 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 2.07 % 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: 0.95 (0.26), residues: 1003 helix: 1.74 (0.25), residues: 367 sheet: 0.09 (0.33), residues: 203 loop : 0.04 (0.32), residues: 433 *********************** 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 202 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 187 average time/residue: 1.0594 time to fit residues: 211.1065 Evaluate side-chains 182 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 173 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 6 average time/residue: 0.3419 time to fit residues: 3.6692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 90 optimal weight: 0.0470 chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 8219 Z= 0.233 Angle : 0.537 5.422 11137 Z= 0.290 Chirality : 0.042 0.167 1252 Planarity : 0.004 0.041 1416 Dihedral : 4.908 24.299 1107 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 2.76 % 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: 1.11 (0.26), residues: 1003 helix: 2.16 (0.26), residues: 365 sheet: -0.09 (0.33), residues: 203 loop : 0.00 (0.32), residues: 435 *********************** 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 216 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 192 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 199 average time/residue: 1.0550 time to fit residues: 224.7363 Evaluate side-chains 189 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 178 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 5 residues processed: 6 average time/residue: 0.1424 time to fit residues: 2.5979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 8219 Z= 0.268 Angle : 0.548 8.332 11137 Z= 0.293 Chirality : 0.043 0.160 1252 Planarity : 0.004 0.045 1416 Dihedral : 4.812 25.915 1107 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 2.76 % 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 (0.27), residues: 1003 helix: 2.27 (0.26), residues: 362 sheet: -0.19 (0.33), residues: 203 loop : -0.14 (0.31), residues: 438 *********************** 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 202 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 0.887 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 191 average time/residue: 1.0703 time to fit residues: 217.7267 Evaluate side-chains 190 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 176 time to evaluate : 0.917 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 7 residues processed: 7 average time/residue: 0.1260 time to fit residues: 2.5526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 0.0870 chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8219 Z= 0.229 Angle : 0.532 8.753 11137 Z= 0.284 Chirality : 0.042 0.157 1252 Planarity : 0.004 0.045 1416 Dihedral : 4.635 24.905 1107 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 2.64 % 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: 0.96 (0.27), residues: 1003 helix: 2.31 (0.26), residues: 364 sheet: -0.38 (0.32), residues: 211 loop : -0.22 (0.31), residues: 428 *********************** 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 200 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 190 average time/residue: 1.0510 time to fit residues: 212.8668 Evaluate side-chains 185 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 172 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.4280 time to fit residues: 4.1833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN R 98 ASN B 156 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 8219 Z= 0.250 Angle : 0.537 7.867 11137 Z= 0.287 Chirality : 0.042 0.153 1252 Planarity : 0.004 0.047 1416 Dihedral : 4.606 23.724 1107 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 3.10 % 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 (0.27), residues: 1003 helix: 2.37 (0.26), residues: 363 sheet: -0.56 (0.32), residues: 214 loop : -0.21 (0.32), residues: 426 *********************** 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 212 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 196 average time/residue: 1.0802 time to fit residues: 225.7425 Evaluate side-chains 193 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 179 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 7 residues processed: 7 average time/residue: 0.1414 time to fit residues: 2.5653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 N 31 ASN B 156 GLN B 293 ASN B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 8219 Z= 0.254 Angle : 0.531 5.740 11137 Z= 0.285 Chirality : 0.042 0.152 1252 Planarity : 0.004 0.047 1416 Dihedral : 4.614 23.708 1107 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 2.64 % 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: 0.90 (0.27), residues: 1003 helix: 2.37 (0.26), residues: 363 sheet: -0.62 (0.32), residues: 214 loop : -0.24 (0.32), residues: 426 *********************** 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 208 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 199 average time/residue: 1.0542 time to fit residues: 223.5617 Evaluate side-chains 197 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 183 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 5 average time/residue: 0.5219 time to fit residues: 4.2678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 60 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 83 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 N 31 ASN B 156 GLN ** B 239 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2682 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= 0.206 Angle : 0.526 8.555 11137 Z= 0.279 Chirality : 0.041 0.172 1252 Planarity : 0.004 0.046 1416 Dihedral : 4.510 22.226 1107 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 2.30 % 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 (0.27), residues: 1003 helix: 2.40 (0.26), residues: 365 sheet: -0.62 (0.32), residues: 214 loop : -0.23 (0.32), residues: 424 *********************** 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 204 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 0.882 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 196 average time/residue: 1.0776 time to fit residues: 224.8030 Evaluate side-chains 194 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 181 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.1417 time to fit residues: 1.6465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 chunk 94 optimal weight: 0.0570 chunk 57 optimal weight: 0.5980 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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 156 GLN B 239 ASN B 293 ASN B 295 ASN ** 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: 0.6942 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8219 Z= 0.198 Angle : 0.511 5.944 11137 Z= 0.273 Chirality : 0.041 0.158 1252 Planarity : 0.004 0.046 1416 Dihedral : 4.423 20.831 1107 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 1.84 % 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: 0.96 (0.27), residues: 1003 helix: 2.47 (0.26), residues: 365 sheet: -0.59 (0.33), residues: 214 loop : -0.27 (0.32), residues: 424 *********************** 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: 16 poor density : 190 time to evaluate : 0.943 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 200 average time/residue: 1.0509 time to fit residues: 224.7946 Evaluate side-chains 202 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 191 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.1456 time to fit residues: 1.7278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.0030 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 30.0000 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 N 35 ASN B 156 GLN B 239 ASN B 293 ASN B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.2790 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= 0.251 Angle : 0.544 8.642 11137 Z= 0.289 Chirality : 0.042 0.182 1252 Planarity : 0.004 0.047 1416 Dihedral : 4.527 21.041 1107 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 1.61 % 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: 2.42 (0.26), residues: 364 sheet: -0.53 (0.34), residues: 203 loop : -0.34 (0.31), residues: 436 ********************** 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 200 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 186 time to evaluate : 0.939 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 196 average time/residue: 1.1365 time to fit residues: 236.3181 Evaluate side-chains 192 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 183 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.0685 time to fit residues: 1.3539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 4 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 R 130 HIS N 35 ASN B 156 GLN B 239 ASN B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.153272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.134349 restraints weight = 10434.062| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.81 r_work: 0.3657 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 8219 Z= 0.200 Angle : 0.517 5.997 11137 Z= 0.277 Chirality : 0.041 0.174 1252 Planarity : 0.004 0.047 1416 Dihedral : 4.432 20.233 1107 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 1003 helix: 2.50 (0.26), residues: 365 sheet: -0.65 (0.33), residues: 216 loop : -0.25 (0.32), residues: 422 =============================================================================== Job complete usr+sys time: 3814.99 seconds wall clock time: 68 minutes 9.69 seconds (4089.69 seconds total)