Starting phenix.real_space_refine on Sat Aug 3 12:42:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg7_37504/08_2024/8wg7_37504.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg7_37504/08_2024/8wg7_37504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg7_37504/08_2024/8wg7_37504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg7_37504/08_2024/8wg7_37504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg7_37504/08_2024/8wg7_37504.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg7_37504/08_2024/8wg7_37504.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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 48 5.16 5 C 5179 2.51 5 N 1412 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "R ARG 348": "NH1" <-> "NH2" Residue "R ARG 380": "NH1" <-> "NH2" Residue "R ARG 421": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8123 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1928 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} 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: "R" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2205 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 5.06, per 1000 atoms: 0.62 Number of scatterers: 8123 At special positions: 0 Unit cell: (74.97, 96.39, 129.591, 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 48 16.00 O 1484 8.00 N 1412 7.00 C 5179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 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: 3.14 Conformation dependent library (CDL) restraints added in 1.7 seconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1942 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.4% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.647A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 279 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 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.783A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.661A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.529A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.955A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 168 Processing helix chain 'R' and resid 174 through 207 removed outlier: 3.918A pdb=" N LEU R 201 " --> pdb=" O LYS R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 223 Processing helix chain 'R' and resid 224 through 257 removed outlier: 3.916A pdb=" N LEU R 228 " --> pdb=" O LEU R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 Processing helix chain 'R' and resid 275 through 292 removed outlier: 3.633A pdb=" N LEU R 279 " --> pdb=" O GLY R 275 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 294 through 298 removed outlier: 3.693A pdb=" N THR R 298 " --> pdb=" O GLY R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 336 removed outlier: 4.407A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 343 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 368 Processing helix chain 'R' and resid 378 through 404 removed outlier: 3.672A pdb=" N ILE R 382 " --> pdb=" O THR R 378 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 424 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.835A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.692A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.028A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.200A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 7.095A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.061A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.714A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.515A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.036A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1281 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: 2.35 Time building geometry restraints manager: 3.47 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: 2610 1.34 - 1.46: 1384 1.46 - 1.58: 4234 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 8294 Sorted by residual: bond pdb=" CA LYS R 346 " pdb=" C LYS R 346 " ideal model delta sigma weight residual 1.527 1.503 0.024 1.21e-02 6.83e+03 4.03e+00 bond pdb=" CA LYS R 336 " pdb=" C LYS R 336 " ideal model delta sigma weight residual 1.526 1.500 0.026 1.36e-02 5.41e+03 3.55e+00 bond pdb=" CA ALA R 337 " pdb=" C ALA R 337 " ideal model delta sigma weight residual 1.523 1.499 0.025 1.34e-02 5.57e+03 3.39e+00 bond pdb=" CA THR R 343 " pdb=" C THR R 343 " ideal model delta sigma weight residual 1.522 1.499 0.023 1.41e-02 5.03e+03 2.61e+00 bond pdb=" CA ASN R 338 " pdb=" C ASN R 338 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.34e-02 5.57e+03 2.43e+00 ... (remaining 8289 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.51: 154 106.51 - 113.37: 4502 113.37 - 120.24: 3022 120.24 - 127.10: 3475 127.10 - 133.96: 85 Bond angle restraints: 11238 Sorted by residual: angle pdb=" N THR R 343 " pdb=" CA THR R 343 " pdb=" C THR R 343 " ideal model delta sigma weight residual 112.38 108.04 4.34 1.22e+00 6.72e-01 1.27e+01 angle pdb=" N ASP R 344 " pdb=" CA ASP R 344 " pdb=" C ASP R 344 " ideal model delta sigma weight residual 111.75 107.93 3.82 1.28e+00 6.10e-01 8.91e+00 angle pdb=" N LEU R 339 " pdb=" CA LEU R 339 " pdb=" C LEU R 339 " ideal model delta sigma weight residual 112.97 110.15 2.82 1.06e+00 8.90e-01 7.07e+00 angle pdb=" C LYS R 336 " pdb=" CA LYS R 336 " pdb=" CB LYS R 336 " ideal model delta sigma weight residual 111.50 108.20 3.30 1.29e+00 6.01e-01 6.54e+00 angle pdb=" N LYS R 346 " pdb=" CA LYS R 346 " pdb=" C LYS R 346 " ideal model delta sigma weight residual 111.56 107.91 3.65 1.53e+00 4.27e-01 5.68e+00 ... (remaining 11233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4485 17.84 - 35.69: 351 35.69 - 53.53: 65 53.53 - 71.38: 8 71.38 - 89.22: 6 Dihedral angle restraints: 4915 sinusoidal: 1913 harmonic: 3002 Sorted by residual: dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual -86.00 -175.22 89.22 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual 180.00 -156.26 -23.74 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA PRO N 41 " pdb=" C PRO N 41 " pdb=" N GLY N 42 " pdb=" CA GLY N 42 " ideal model delta harmonic sigma weight residual -180.00 -160.23 -19.77 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 4912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 809 0.033 - 0.066: 311 0.066 - 0.100: 104 0.100 - 0.133: 37 0.133 - 0.166: 6 Chirality restraints: 1267 Sorted by residual: chirality pdb=" CA GLN A 19 " pdb=" N GLN A 19 " pdb=" C GLN A 19 " pdb=" CB GLN A 19 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA TYR R 152 " pdb=" N TYR R 152 " pdb=" C TYR R 152 " pdb=" CB TYR R 152 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1264 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO A 332 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO G 53 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA N 40 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO N 41 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO N 41 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO N 41 " -0.024 5.00e-02 4.00e+02 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 263 2.71 - 3.26: 8170 3.26 - 3.81: 13475 3.81 - 4.35: 16401 4.35 - 4.90: 28505 Nonbonded interactions: 66814 Sorted by model distance: nonbonded pdb=" NE2 GLN A 59 " pdb=" O ASP A 368 " model vdw 2.167 3.120 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.229 3.120 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.244 3.040 nonbonded pdb=" OG SER R 136 " pdb=" OE1 GLU R 138 " model vdw 2.265 3.040 nonbonded pdb=" NH1 ARG B 251 " pdb=" OE2 GLU B 260 " model vdw 2.269 3.120 ... (remaining 66809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.280 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8294 Z= 0.182 Angle : 0.542 6.432 11238 Z= 0.325 Chirality : 0.042 0.166 1267 Planarity : 0.004 0.060 1424 Dihedral : 13.039 87.080 2964 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.55 % Favored : 96.15 % Rotamer: Outliers : 0.12 % Allowed : 0.58 % Favored : 99.30 % 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: 1.50 (0.27), residues: 1014 helix: 2.83 (0.27), residues: 379 sheet: 0.42 (0.34), residues: 230 loop : -0.44 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.010 0.001 PHE A 212 TYR 0.022 0.001 TYR R 152 ARG 0.009 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 0.898 Fit side-chains REVERT: A 15 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6796 (mm-30) REVERT: A 19 GLN cc_start: 0.7260 (mp10) cc_final: 0.6773 (mp10) REVERT: A 35 GLN cc_start: 0.8196 (tt0) cc_final: 0.7974 (tt0) REVERT: B 175 GLN cc_start: 0.8041 (pp30) cc_final: 0.7818 (pp30) REVERT: G 21 MET cc_start: 0.6486 (ttp) cc_final: 0.6199 (tmt) REVERT: N 31 ASN cc_start: 0.8369 (m110) cc_final: 0.8134 (m110) REVERT: N 87 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8639 (mtpm) REVERT: N 106 ASP cc_start: 0.8552 (p0) cc_final: 0.8118 (p0) REVERT: R 139 GLU cc_start: 0.7668 (pm20) cc_final: 0.6927 (pm20) REVERT: R 306 TRP cc_start: 0.8652 (t60) cc_final: 0.8257 (t-100) REVERT: R 418 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8156 (mm-30) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 1.4315 time to fit residues: 263.0514 Evaluate side-chains 137 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.0270 chunk 75 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 279 ASN N 31 ASN N 39 GLN N 77 ASN R 180 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8294 Z= 0.195 Angle : 0.554 7.582 11238 Z= 0.299 Chirality : 0.042 0.165 1267 Planarity : 0.004 0.054 1424 Dihedral : 4.014 19.307 1124 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.32 % Allowed : 13.21 % Favored : 84.47 % 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: 1.60 (0.27), residues: 1014 helix: 2.98 (0.26), residues: 376 sheet: 0.33 (0.34), residues: 232 loop : -0.34 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.014 0.001 TYR R 148 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8362 (tm-30) cc_final: 0.8130 (tt0) REVERT: B 175 GLN cc_start: 0.8084 (pp30) cc_final: 0.7850 (pp30) REVERT: G 21 MET cc_start: 0.6531 (ttp) cc_final: 0.6161 (tmt) REVERT: N 31 ASN cc_start: 0.8368 (m-40) cc_final: 0.8106 (m110) REVERT: N 53 GLN cc_start: 0.8336 (mp10) cc_final: 0.8022 (mp10) REVERT: N 87 LYS cc_start: 0.8811 (mtpt) cc_final: 0.8540 (mtpm) REVERT: N 104 THR cc_start: 0.8458 (t) cc_final: 0.8217 (t) REVERT: N 106 ASP cc_start: 0.8831 (p0) cc_final: 0.8354 (p0) REVERT: R 139 GLU cc_start: 0.7757 (pm20) cc_final: 0.7250 (pm20) REVERT: R 306 TRP cc_start: 0.8381 (t60) cc_final: 0.8039 (t-100) REVERT: R 423 GLU cc_start: 0.8362 (pp20) cc_final: 0.8158 (pp20) outliers start: 20 outliers final: 6 residues processed: 156 average time/residue: 1.2269 time to fit residues: 202.5535 Evaluate side-chains 143 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 0.1980 chunk 98 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN A 64 HIS N 39 GLN N 77 ASN R 320 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8294 Z= 0.223 Angle : 0.546 7.603 11238 Z= 0.295 Chirality : 0.042 0.131 1267 Planarity : 0.004 0.050 1424 Dihedral : 4.051 19.980 1124 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.90 % Allowed : 15.53 % Favored : 81.58 % 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: 1.66 (0.27), residues: 1014 helix: 3.03 (0.26), residues: 376 sheet: 0.23 (0.34), residues: 235 loop : -0.20 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 420 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE R 169 TYR 0.016 0.001 TYR R 148 ARG 0.005 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7460 (pm20) cc_final: 0.7013 (pm20) REVERT: B 175 GLN cc_start: 0.8166 (pp30) cc_final: 0.7832 (pp30) REVERT: B 301 LYS cc_start: 0.8444 (mmmt) cc_final: 0.8224 (mmmt) REVERT: G 21 MET cc_start: 0.6566 (ttp) cc_final: 0.6140 (tmt) REVERT: N 31 ASN cc_start: 0.8350 (m-40) cc_final: 0.8119 (m-40) REVERT: N 53 GLN cc_start: 0.8364 (mp10) cc_final: 0.8059 (mp10) REVERT: N 87 LYS cc_start: 0.8747 (mtpt) cc_final: 0.8308 (mtpm) REVERT: N 104 THR cc_start: 0.8696 (t) cc_final: 0.8468 (t) REVERT: N 105 ARG cc_start: 0.8266 (ttp-110) cc_final: 0.8055 (ttp-110) REVERT: N 106 ASP cc_start: 0.8868 (p0) cc_final: 0.8540 (p0) REVERT: R 139 GLU cc_start: 0.7788 (pm20) cc_final: 0.7382 (pm20) REVERT: R 197 LYS cc_start: 0.8844 (tmtm) cc_final: 0.8559 (tmmm) REVERT: R 233 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7616 (tmt) REVERT: R 262 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7354 (pm20) REVERT: R 306 TRP cc_start: 0.8386 (t60) cc_final: 0.8063 (t-100) REVERT: R 387 GLU cc_start: 0.7350 (tp30) cc_final: 0.7109 (tp30) outliers start: 25 outliers final: 12 residues processed: 157 average time/residue: 1.3071 time to fit residues: 216.8002 Evaluate side-chains 147 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN A 64 HIS A 390 GLN N 39 GLN N 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8294 Z= 0.215 Angle : 0.547 7.820 11238 Z= 0.295 Chirality : 0.042 0.131 1267 Planarity : 0.004 0.049 1424 Dihedral : 4.057 20.512 1124 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.82 % Allowed : 16.45 % Favored : 79.72 % 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: 1.62 (0.27), residues: 1014 helix: 3.02 (0.26), residues: 377 sheet: 0.15 (0.32), residues: 242 loop : -0.22 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 420 HIS 0.004 0.001 HIS A 357 PHE 0.021 0.001 PHE R 169 TYR 0.017 0.001 TYR R 148 ARG 0.009 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 144 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8199 (pp30) cc_final: 0.7812 (pp30) REVERT: B 301 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8202 (mmmt) REVERT: G 21 MET cc_start: 0.6622 (ttp) cc_final: 0.6177 (tmt) REVERT: N 31 ASN cc_start: 0.8383 (m-40) cc_final: 0.8139 (m-40) REVERT: N 53 GLN cc_start: 0.8375 (mp10) cc_final: 0.8047 (mp10) REVERT: N 87 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8496 (mtpm) REVERT: N 104 THR cc_start: 0.8784 (t) cc_final: 0.8537 (t) REVERT: N 105 ARG cc_start: 0.8296 (ttp-110) cc_final: 0.8081 (ttp-110) REVERT: N 106 ASP cc_start: 0.8850 (p0) cc_final: 0.8556 (p0) REVERT: R 139 GLU cc_start: 0.7789 (pm20) cc_final: 0.7346 (pm20) REVERT: R 197 LYS cc_start: 0.8846 (tmtm) cc_final: 0.8534 (tmmm) REVERT: R 262 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7365 (pm20) REVERT: R 306 TRP cc_start: 0.8389 (t60) cc_final: 0.8029 (t-100) REVERT: R 362 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8249 (m) REVERT: R 387 GLU cc_start: 0.7410 (tp30) cc_final: 0.7204 (tp30) REVERT: R 423 GLU cc_start: 0.8373 (pp20) cc_final: 0.8164 (pp20) outliers start: 33 outliers final: 16 residues processed: 160 average time/residue: 1.2521 time to fit residues: 211.9372 Evaluate side-chains 149 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 0.0060 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN A 64 HIS A 390 GLN N 39 GLN N 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8294 Z= 0.199 Angle : 0.549 7.700 11238 Z= 0.294 Chirality : 0.042 0.135 1267 Planarity : 0.004 0.048 1424 Dihedral : 4.038 20.494 1124 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.48 % Allowed : 18.19 % Favored : 78.33 % 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: 1.62 (0.27), residues: 1014 helix: 3.04 (0.26), residues: 378 sheet: 0.09 (0.32), residues: 242 loop : -0.21 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 420 HIS 0.003 0.001 HIS R 363 PHE 0.014 0.001 PHE R 169 TYR 0.015 0.001 TYR R 148 ARG 0.010 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 147 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8204 (pp30) cc_final: 0.7759 (pp30) REVERT: B 243 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7814 (p) REVERT: B 301 LYS cc_start: 0.8383 (mmmt) cc_final: 0.8119 (mmmt) REVERT: G 21 MET cc_start: 0.6634 (ttp) cc_final: 0.6171 (tmt) REVERT: N 31 ASN cc_start: 0.8309 (m-40) cc_final: 0.8071 (m-40) REVERT: N 53 GLN cc_start: 0.8357 (mp10) cc_final: 0.8020 (mp10) REVERT: N 87 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8514 (mtpm) REVERT: N 104 THR cc_start: 0.8807 (t) cc_final: 0.8555 (t) REVERT: N 105 ARG cc_start: 0.8310 (ttp-110) cc_final: 0.8094 (ttp-110) REVERT: N 106 ASP cc_start: 0.8833 (p0) cc_final: 0.8594 (p0) REVERT: R 138 GLU cc_start: 0.7914 (pm20) cc_final: 0.7666 (pm20) REVERT: R 139 GLU cc_start: 0.7801 (pm20) cc_final: 0.7442 (pm20) REVERT: R 197 LYS cc_start: 0.8875 (tmtm) cc_final: 0.8536 (tmmm) REVERT: R 306 TRP cc_start: 0.8384 (t60) cc_final: 0.8004 (t-100) REVERT: R 362 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8277 (m) outliers start: 30 outliers final: 17 residues processed: 164 average time/residue: 1.2494 time to fit residues: 216.7592 Evaluate side-chains 152 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 80 optimal weight: 0.1980 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN A 64 HIS A 390 GLN N 39 GLN N 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8294 Z= 0.209 Angle : 0.566 9.086 11238 Z= 0.301 Chirality : 0.042 0.146 1267 Planarity : 0.004 0.049 1424 Dihedral : 4.036 20.888 1124 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.06 % Allowed : 18.54 % Favored : 77.40 % 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: 1.63 (0.27), residues: 1014 helix: 3.07 (0.26), residues: 378 sheet: 0.05 (0.32), residues: 242 loop : -0.20 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 420 HIS 0.004 0.001 HIS R 363 PHE 0.012 0.001 PHE A 212 TYR 0.015 0.001 TYR R 148 ARG 0.012 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 136 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8208 (pp30) cc_final: 0.7727 (pp30) REVERT: B 243 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7821 (p) REVERT: G 21 MET cc_start: 0.6653 (ttp) cc_final: 0.6128 (tmt) REVERT: N 31 ASN cc_start: 0.8368 (m-40) cc_final: 0.8112 (m-40) REVERT: N 53 GLN cc_start: 0.8416 (mp10) cc_final: 0.8069 (mp10) REVERT: N 87 LYS cc_start: 0.8739 (mtpt) cc_final: 0.8358 (mtpm) REVERT: N 105 ARG cc_start: 0.8354 (ttp-110) cc_final: 0.8104 (ttp-110) REVERT: R 138 GLU cc_start: 0.7876 (pm20) cc_final: 0.7609 (pm20) REVERT: R 139 GLU cc_start: 0.7860 (pm20) cc_final: 0.7423 (pm20) REVERT: R 197 LYS cc_start: 0.8880 (tmtm) cc_final: 0.8541 (tmmm) REVERT: R 306 TRP cc_start: 0.8379 (t60) cc_final: 0.8023 (t-100) REVERT: R 362 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8311 (m) outliers start: 35 outliers final: 18 residues processed: 156 average time/residue: 1.2645 time to fit residues: 208.5345 Evaluate side-chains 154 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN A 64 HIS A 390 GLN N 39 GLN N 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8294 Z= 0.217 Angle : 0.576 9.270 11238 Z= 0.305 Chirality : 0.042 0.152 1267 Planarity : 0.004 0.056 1424 Dihedral : 4.065 20.768 1124 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.94 % Allowed : 19.81 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.27), residues: 1014 helix: 3.08 (0.26), residues: 378 sheet: 0.03 (0.32), residues: 242 loop : -0.22 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 420 HIS 0.005 0.001 HIS R 363 PHE 0.013 0.001 PHE A 212 TYR 0.014 0.001 TYR R 148 ARG 0.013 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 137 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 ARG cc_start: 0.8153 (mpp80) cc_final: 0.7901 (mtm-85) REVERT: B 175 GLN cc_start: 0.8217 (pp30) cc_final: 0.7720 (pp30) REVERT: B 217 MET cc_start: 0.8220 (ppp) cc_final: 0.7987 (ppp) REVERT: B 243 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7823 (p) REVERT: G 21 MET cc_start: 0.6652 (ttp) cc_final: 0.6403 (ttt) REVERT: N 31 ASN cc_start: 0.8401 (m-40) cc_final: 0.8147 (m-40) REVERT: N 53 GLN cc_start: 0.8385 (mp10) cc_final: 0.8034 (mp10) REVERT: N 87 LYS cc_start: 0.8741 (mtpt) cc_final: 0.8358 (mtpm) REVERT: N 105 ARG cc_start: 0.8338 (ttp-110) cc_final: 0.8096 (ttp-110) REVERT: N 125 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8786 (p) REVERT: R 138 GLU cc_start: 0.7864 (pm20) cc_final: 0.7583 (pm20) REVERT: R 139 GLU cc_start: 0.7872 (pm20) cc_final: 0.7398 (pm20) REVERT: R 197 LYS cc_start: 0.8882 (tmtm) cc_final: 0.8541 (tmmm) REVERT: R 306 TRP cc_start: 0.8399 (t60) cc_final: 0.8027 (t-100) REVERT: R 362 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8324 (m) outliers start: 34 outliers final: 17 residues processed: 159 average time/residue: 1.2353 time to fit residues: 207.7038 Evaluate side-chains 152 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 0.0170 chunk 84 optimal weight: 0.0670 chunk 89 optimal weight: 0.9980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN A 64 HIS N 39 GLN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8294 Z= 0.180 Angle : 0.588 13.129 11238 Z= 0.305 Chirality : 0.042 0.158 1267 Planarity : 0.004 0.059 1424 Dihedral : 4.020 20.518 1124 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.90 % Allowed : 21.67 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.27), residues: 1014 helix: 3.10 (0.26), residues: 378 sheet: 0.01 (0.32), residues: 242 loop : -0.22 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 420 HIS 0.005 0.001 HIS R 363 PHE 0.012 0.001 PHE A 212 TYR 0.013 0.001 TYR A 311 ARG 0.014 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.9341 (mp) cc_final: 0.9104 (mt) REVERT: A 317 ARG cc_start: 0.8263 (mtm-85) cc_final: 0.7968 (mtm-85) REVERT: A 356 ARG cc_start: 0.8091 (mpp80) cc_final: 0.7818 (mtm-85) REVERT: B 175 GLN cc_start: 0.8209 (pp30) cc_final: 0.7780 (pp30) REVERT: B 243 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7787 (p) REVERT: G 21 MET cc_start: 0.6696 (ttp) cc_final: 0.6327 (tmm) REVERT: N 31 ASN cc_start: 0.8319 (m-40) cc_final: 0.8048 (m-40) REVERT: N 53 GLN cc_start: 0.8378 (mp10) cc_final: 0.8019 (mp10) REVERT: N 87 LYS cc_start: 0.8738 (mtpt) cc_final: 0.8331 (mtpm) REVERT: N 105 ARG cc_start: 0.8347 (ttp-110) cc_final: 0.8097 (ttp-110) REVERT: N 125 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8785 (p) REVERT: R 138 GLU cc_start: 0.7865 (pm20) cc_final: 0.7582 (pm20) REVERT: R 139 GLU cc_start: 0.7889 (pm20) cc_final: 0.7404 (pm20) REVERT: R 197 LYS cc_start: 0.8927 (tmtm) cc_final: 0.8572 (tmmm) REVERT: R 306 TRP cc_start: 0.8368 (t60) cc_final: 0.7962 (t-100) REVERT: R 362 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8301 (m) outliers start: 25 outliers final: 15 residues processed: 157 average time/residue: 1.2479 time to fit residues: 207.6083 Evaluate side-chains 152 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.0770 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 0.0020 chunk 89 optimal weight: 0.0670 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 0.0670 chunk 57 optimal weight: 0.0870 overall best weight: 0.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN A 64 HIS A 390 GLN B 110 ASN B 237 ASN B 239 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 77 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8294 Z= 0.147 Angle : 0.595 14.250 11238 Z= 0.304 Chirality : 0.042 0.194 1267 Planarity : 0.004 0.059 1424 Dihedral : 3.959 22.048 1124 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.62 % Allowed : 23.17 % Favored : 75.20 % 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: 1.63 (0.27), residues: 1014 helix: 3.25 (0.26), residues: 372 sheet: -0.06 (0.31), residues: 243 loop : -0.25 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 420 HIS 0.011 0.001 HIS R 424 PHE 0.012 0.001 PHE A 212 TYR 0.016 0.001 TYR A 253 ARG 0.015 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8365 (tm-30) cc_final: 0.8054 (mt0) REVERT: A 314 GLU cc_start: 0.7878 (pm20) cc_final: 0.7620 (pm20) REVERT: B 175 GLN cc_start: 0.8240 (pp30) cc_final: 0.7823 (pp30) REVERT: B 243 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7676 (p) REVERT: B 336 LEU cc_start: 0.8746 (mt) cc_final: 0.8426 (mt) REVERT: G 21 MET cc_start: 0.6775 (ttp) cc_final: 0.6353 (tmm) REVERT: N 34 MET cc_start: 0.8365 (mmm) cc_final: 0.8056 (mmm) REVERT: N 53 GLN cc_start: 0.8288 (mp10) cc_final: 0.7944 (mp10) REVERT: N 87 LYS cc_start: 0.8823 (mtpt) cc_final: 0.8574 (mtpm) REVERT: N 105 ARG cc_start: 0.8227 (ttp-110) cc_final: 0.7993 (ttp-110) REVERT: N 125 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8774 (p) REVERT: R 138 GLU cc_start: 0.7858 (pm20) cc_final: 0.7577 (pm20) REVERT: R 139 GLU cc_start: 0.7889 (pm20) cc_final: 0.7395 (pm20) REVERT: R 197 LYS cc_start: 0.8926 (tmtm) cc_final: 0.8607 (tmmm) REVERT: R 262 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7285 (pm20) REVERT: R 292 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7677 (tp30) REVERT: R 306 TRP cc_start: 0.8326 (t60) cc_final: 0.8075 (t-100) REVERT: R 362 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8223 (m) outliers start: 14 outliers final: 6 residues processed: 163 average time/residue: 1.2163 time to fit residues: 209.8850 Evaluate side-chains 154 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 0.0370 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN A 64 HIS A 220 HIS A 390 GLN B 237 ASN N 39 GLN R 182 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8294 Z= 0.193 Angle : 0.609 13.023 11238 Z= 0.315 Chirality : 0.043 0.188 1267 Planarity : 0.004 0.045 1424 Dihedral : 4.009 25.821 1124 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.09 % Allowed : 23.06 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.27), residues: 1014 helix: 3.26 (0.26), residues: 372 sheet: 0.05 (0.32), residues: 236 loop : -0.32 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 420 HIS 0.006 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.018 0.001 TYR R 269 ARG 0.009 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLU cc_start: 0.7941 (pm20) cc_final: 0.7697 (pm20) REVERT: B 175 GLN cc_start: 0.8183 (pp30) cc_final: 0.7779 (pp30) REVERT: B 243 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7786 (p) REVERT: G 21 MET cc_start: 0.6718 (ttp) cc_final: 0.6351 (tmm) REVERT: N 53 GLN cc_start: 0.8284 (mp10) cc_final: 0.7930 (mp10) REVERT: N 87 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8508 (mtpm) REVERT: N 105 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7925 (ttp-110) REVERT: N 125 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8802 (p) REVERT: R 138 GLU cc_start: 0.7861 (pm20) cc_final: 0.7577 (pm20) REVERT: R 139 GLU cc_start: 0.7893 (pm20) cc_final: 0.7405 (pm20) REVERT: R 197 LYS cc_start: 0.8943 (tmtm) cc_final: 0.8594 (tmmm) REVERT: R 262 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7262 (pm20) REVERT: R 292 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7653 (tp30) REVERT: R 362 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8298 (m) outliers start: 18 outliers final: 9 residues processed: 153 average time/residue: 1.2691 time to fit residues: 205.4086 Evaluate side-chains 155 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN A 390 GLN B 239 ASN N 31 ASN N 39 GLN ** R 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.126967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.090833 restraints weight = 11996.948| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.92 r_work: 0.3041 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.240 8294 Z= 0.350 Angle : 1.024 59.181 11238 Z= 0.650 Chirality : 0.058 1.033 1267 Planarity : 0.008 0.213 1424 Dihedral : 4.107 25.347 1124 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.62 % Allowed : 23.52 % Favored : 74.86 % Cbeta Deviations : 0.21 % 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: 1.59 (0.27), residues: 1014 helix: 3.19 (0.26), residues: 372 sheet: 0.06 (0.32), residues: 236 loop : -0.35 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 420 HIS 0.019 0.002 HIS R 424 PHE 0.014 0.001 PHE R 367 TYR 0.017 0.001 TYR R 269 ARG 0.008 0.000 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3856.28 seconds wall clock time: 67 minutes 48.14 seconds (4068.14 seconds total)