Starting phenix.real_space_refine on Sat Apr 6 11:35:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg7_37504/04_2024/8wg7_37504.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg7_37504/04_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_37504/04_2024/8wg7_37504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg7_37504/04_2024/8wg7_37504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg7_37504/04_2024/8wg7_37504.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg7_37504/04_2024/8wg7_37504.pdb" } 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-5288/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: 4.76, per 1000 atoms: 0.59 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: 3.01 Conformation dependent library (CDL) restraints added in 1.5 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: 0.90 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: 2.47 Time building geometry restraints manager: 3.27 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 2.520 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.229 2.520 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.244 2.440 nonbonded pdb=" OG SER R 136 " pdb=" OE1 GLU R 138 " model vdw 2.265 2.440 nonbonded pdb=" NH1 ARG B 251 " pdb=" OE2 GLU B 260 " model vdw 2.269 2.520 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 3.930 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 25.250 Find NCS groups from input model: 0.230 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:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.400 ------------------------------------------------------------------------------- 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 : 0.987 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: 1.4580 time to fit residues: 267.9013 Evaluate side-chains 137 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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: 0.0570 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.0870 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 64 HIS A 279 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7557 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8294 Z= 0.162 Angle : 0.531 7.781 11238 Z= 0.285 Chirality : 0.041 0.155 1267 Planarity : 0.004 0.053 1424 Dihedral : 3.954 19.192 1124 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.09 % Allowed : 13.56 % Favored : 84.36 % 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: 1.64 (0.27), residues: 1014 helix: 3.03 (0.26), residues: 376 sheet: 0.36 (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 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.014 0.001 TYR R 148 ARG 0.007 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 161 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8344 (tm-30) cc_final: 0.8141 (tt0) REVERT: B 175 GLN cc_start: 0.8146 (pp30) cc_final: 0.7887 (pp30) REVERT: G 21 MET cc_start: 0.6542 (ttp) cc_final: 0.6190 (tmt) REVERT: N 31 ASN cc_start: 0.8330 (m110) cc_final: 0.8124 (m110) REVERT: N 87 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8508 (mtpm) REVERT: N 106 ASP cc_start: 0.8680 (p0) cc_final: 0.8272 (p0) REVERT: R 139 GLU cc_start: 0.7699 (pm20) cc_final: 0.7256 (pm20) REVERT: R 306 TRP cc_start: 0.8360 (t60) cc_final: 0.8001 (t-100) outliers start: 18 outliers final: 5 residues processed: 150 average time/residue: 1.2664 time to fit residues: 201.3260 Evaluate side-chains 135 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 307 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: 0.0980 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN B 88 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8294 Z= 0.151 Angle : 0.504 7.828 11238 Z= 0.271 Chirality : 0.041 0.142 1267 Planarity : 0.004 0.049 1424 Dihedral : 3.892 19.006 1124 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.43 % Allowed : 15.99 % 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: 1.69 (0.27), residues: 1014 helix: 3.12 (0.26), residues: 376 sheet: 0.28 (0.34), residues: 234 loop : -0.28 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.003 0.001 HIS R 363 PHE 0.015 0.001 PHE R 169 TYR 0.014 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 162 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8181 (pp30) cc_final: 0.7865 (pp30) REVERT: B 301 LYS cc_start: 0.8324 (mmmt) cc_final: 0.8113 (mmmt) REVERT: G 21 MET cc_start: 0.6525 (ttp) cc_final: 0.6154 (tmt) REVERT: N 31 ASN cc_start: 0.8335 (m110) cc_final: 0.8075 (m110) REVERT: N 87 LYS cc_start: 0.8749 (mtpt) cc_final: 0.8371 (mtpm) REVERT: N 106 ASP cc_start: 0.8775 (p0) cc_final: 0.8475 (p0) REVERT: R 139 GLU cc_start: 0.7673 (pm20) cc_final: 0.7248 (pm20) REVERT: R 197 LYS cc_start: 0.8858 (tmtm) cc_final: 0.8568 (tmmm) REVERT: R 262 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: R 306 TRP cc_start: 0.8377 (t60) cc_final: 0.8066 (t-100) REVERT: R 387 GLU cc_start: 0.7442 (tp30) cc_final: 0.7197 (tp30) outliers start: 21 outliers final: 10 residues processed: 150 average time/residue: 1.3662 time to fit residues: 216.2245 Evaluate side-chains 145 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 HIS 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 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 262 GLU 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: 2.9990 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 88 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 77 ASN R 320 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 8294 Z= 0.463 Angle : 0.655 8.257 11238 Z= 0.351 Chirality : 0.047 0.153 1267 Planarity : 0.005 0.051 1424 Dihedral : 4.439 22.400 1124 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.17 % Allowed : 17.38 % Favored : 78.45 % 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: 1.41 (0.27), residues: 1014 helix: 2.69 (0.26), residues: 384 sheet: 0.21 (0.33), residues: 233 loop : -0.34 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.008 0.002 HIS A 357 PHE 0.016 0.002 PHE R 367 TYR 0.026 0.002 TYR N 32 ARG 0.009 0.001 ARG N 105 *********************** 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 170 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7476 (pm20) cc_final: 0.7155 (pm20) REVERT: B 175 GLN cc_start: 0.8280 (pp30) cc_final: 0.7902 (pp30) REVERT: G 21 MET cc_start: 0.6788 (ttp) cc_final: 0.6396 (tmt) REVERT: N 31 ASN cc_start: 0.8621 (m110) cc_final: 0.8302 (m110) REVERT: N 67 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7966 (ttp80) REVERT: N 87 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8277 (mtpm) REVERT: R 138 GLU cc_start: 0.7705 (pm20) cc_final: 0.7459 (pm20) REVERT: R 139 GLU cc_start: 0.7666 (pm20) cc_final: 0.7241 (pm20) REVERT: R 197 LYS cc_start: 0.8876 (tmtm) cc_final: 0.8546 (tmmm) REVERT: R 262 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7386 (pm20) REVERT: R 306 TRP cc_start: 0.8408 (t60) cc_final: 0.8056 (t-100) REVERT: R 420 TRP cc_start: 0.7151 (t60) cc_final: 0.6933 (t60) outliers start: 36 outliers final: 21 residues processed: 156 average time/residue: 1.4202 time to fit residues: 233.6751 Evaluate side-chains 146 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 83 MET 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 194 VAL 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 365 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 0.3980 chunk 87 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2029 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 : 0.548 8.293 11238 Z= 0.293 Chirality : 0.042 0.130 1267 Planarity : 0.004 0.049 1424 Dihedral : 4.203 21.521 1124 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.90 % Allowed : 20.39 % Favored : 76.71 % 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: 1.48 (0.27), residues: 1014 helix: 2.96 (0.26), residues: 378 sheet: 0.10 (0.33), residues: 226 loop : -0.39 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS R 363 PHE 0.022 0.001 PHE R 169 TYR 0.017 0.001 TYR N 32 ARG 0.009 0.000 ARG N 105 *********************** 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 156 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ARG cc_start: 0.7552 (mtm110) cc_final: 0.7347 (mtp-110) REVERT: B 175 GLN cc_start: 0.8301 (pp30) cc_final: 0.7812 (pp30) REVERT: G 21 MET cc_start: 0.6514 (ttp) cc_final: 0.6259 (tmt) REVERT: N 67 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7935 (ttp80) REVERT: N 87 LYS cc_start: 0.8721 (mtpt) cc_final: 0.8341 (mtpm) REVERT: R 138 GLU cc_start: 0.7723 (pm20) cc_final: 0.7495 (pm20) REVERT: R 139 GLU cc_start: 0.7689 (pm20) cc_final: 0.7199 (pm20) REVERT: R 197 LYS cc_start: 0.8880 (tmtm) cc_final: 0.8536 (tmmm) REVERT: R 306 TRP cc_start: 0.8394 (t60) cc_final: 0.7969 (t-100) REVERT: R 420 TRP cc_start: 0.7150 (t60) cc_final: 0.6913 (t60) outliers start: 25 outliers final: 17 residues processed: 148 average time/residue: 1.3329 time to fit residues: 208.4004 Evaluate side-chains 140 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL 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 232 LEU Chi-restraints excluded: chain R residue 320 ASN 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: 6.9990 chunk 23 optimal weight: 0.0010 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 88 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8294 Z= 0.162 Angle : 0.536 9.098 11238 Z= 0.286 Chirality : 0.041 0.149 1267 Planarity : 0.004 0.050 1424 Dihedral : 4.072 21.015 1124 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.01 % Allowed : 21.55 % 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: 1.64 (0.27), residues: 1014 helix: 3.20 (0.26), residues: 372 sheet: 0.09 (0.33), residues: 226 loop : -0.28 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS R 363 PHE 0.015 0.001 PHE R 169 TYR 0.013 0.001 TYR R 148 ARG 0.013 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 160 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8272 (pp30) cc_final: 0.7775 (pp30) REVERT: G 21 MET cc_start: 0.6615 (ttp) cc_final: 0.6221 (tmt) REVERT: N 87 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8353 (mtpm) REVERT: R 138 GLU cc_start: 0.7745 (pm20) cc_final: 0.7510 (pm20) REVERT: R 139 GLU cc_start: 0.7720 (pm20) cc_final: 0.7238 (pm20) REVERT: R 197 LYS cc_start: 0.8881 (tmtm) cc_final: 0.8543 (tmmm) REVERT: R 262 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7315 (pm20) REVERT: R 306 TRP cc_start: 0.8406 (t60) cc_final: 0.8041 (t-100) REVERT: R 420 TRP cc_start: 0.7116 (t60) cc_final: 0.6878 (t60) outliers start: 26 outliers final: 20 residues processed: 151 average time/residue: 1.3512 time to fit residues: 215.3569 Evaluate side-chains 146 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 241 VAL 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 84 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL 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 262 GLU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 320 ASN Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 397 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 60 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 390 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8294 Z= 0.209 Angle : 0.558 9.272 11238 Z= 0.297 Chirality : 0.042 0.155 1267 Planarity : 0.004 0.057 1424 Dihedral : 4.068 20.979 1124 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.06 % Allowed : 20.97 % Favored : 74.97 % 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: 3.22 (0.26), residues: 372 sheet: 0.09 (0.33), residues: 226 loop : -0.27 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.005 0.001 HIS R 363 PHE 0.014 0.001 PHE R 169 TYR 0.015 0.001 TYR N 32 ARG 0.015 0.001 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 168 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8287 (pp30) cc_final: 0.7769 (pp30) REVERT: G 21 MET cc_start: 0.6853 (ttp) cc_final: 0.6367 (tmt) REVERT: N 87 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8326 (mtpm) REVERT: N 125 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8768 (p) REVERT: R 138 GLU cc_start: 0.7779 (pm20) cc_final: 0.7539 (pm20) REVERT: R 139 GLU cc_start: 0.7725 (pm20) cc_final: 0.7225 (pm20) REVERT: R 197 LYS cc_start: 0.8895 (tmtm) cc_final: 0.8555 (tmmm) REVERT: R 262 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7306 (pm20) REVERT: R 306 TRP cc_start: 0.8405 (t60) cc_final: 0.7993 (t-100) REVERT: R 420 TRP cc_start: 0.7120 (t60) cc_final: 0.6846 (t60) outliers start: 35 outliers final: 22 residues processed: 156 average time/residue: 1.2970 time to fit residues: 214.1860 Evaluate side-chains 150 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL 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 84 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 52 THR 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 262 GLU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 320 ASN Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 397 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 92 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.1980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8294 Z= 0.187 Angle : 0.580 13.583 11238 Z= 0.301 Chirality : 0.042 0.160 1267 Planarity : 0.004 0.059 1424 Dihedral : 4.087 20.836 1124 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.48 % Allowed : 21.55 % Favored : 74.97 % 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: 1.71 (0.27), residues: 1014 helix: 3.27 (0.26), residues: 372 sheet: 0.11 (0.33), residues: 226 loop : -0.25 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.005 0.001 HIS R 363 PHE 0.012 0.001 PHE A 212 TYR 0.013 0.001 TYR R 148 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 163 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.9356 (mp) cc_final: 0.9128 (mt) REVERT: B 175 GLN cc_start: 0.8274 (pp30) cc_final: 0.7748 (pp30) REVERT: G 21 MET cc_start: 0.6641 (ttp) cc_final: 0.6391 (ttt) REVERT: N 87 LYS cc_start: 0.8747 (mtpt) cc_final: 0.8349 (mtpm) REVERT: N 125 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8786 (p) REVERT: R 138 GLU cc_start: 0.7778 (pm20) cc_final: 0.7536 (pm20) REVERT: R 139 GLU cc_start: 0.7728 (pm20) cc_final: 0.7211 (pm20) REVERT: R 197 LYS cc_start: 0.8912 (tmtm) cc_final: 0.8570 (tmmm) REVERT: R 262 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: R 306 TRP cc_start: 0.8392 (t60) cc_final: 0.7969 (t-100) REVERT: R 420 TRP cc_start: 0.7107 (t60) cc_final: 0.6863 (t60) outliers start: 30 outliers final: 21 residues processed: 155 average time/residue: 1.2983 time to fit residues: 212.7726 Evaluate side-chains 152 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 52 THR 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 262 GLU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 320 ASN 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: 0.0980 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.0020 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 39 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8294 Z= 0.167 Angle : 0.575 14.157 11238 Z= 0.296 Chirality : 0.042 0.191 1267 Planarity : 0.004 0.061 1424 Dihedral : 4.010 20.270 1124 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: 1.75 (0.28), residues: 1014 helix: 3.33 (0.26), residues: 372 sheet: 0.13 (0.33), residues: 226 loop : -0.26 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.006 0.001 HIS R 363 PHE 0.011 0.001 PHE A 212 TYR 0.013 0.001 TYR R 148 ARG 0.015 0.001 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 157 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7944 (mt0) REVERT: B 175 GLN cc_start: 0.8261 (pp30) cc_final: 0.7737 (pp30) REVERT: G 21 MET cc_start: 0.6822 (ttp) cc_final: 0.6365 (tmm) REVERT: N 87 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8430 (mtpm) REVERT: N 125 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8779 (p) REVERT: R 138 GLU cc_start: 0.7839 (pm20) cc_final: 0.7585 (pm20) REVERT: R 139 GLU cc_start: 0.7726 (pm20) cc_final: 0.7200 (pm20) REVERT: R 197 LYS cc_start: 0.8923 (tmtm) cc_final: 0.8571 (tmmm) REVERT: R 262 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: R 306 TRP cc_start: 0.8353 (t60) cc_final: 0.8069 (t-100) outliers start: 25 outliers final: 19 residues processed: 150 average time/residue: 1.4221 time to fit residues: 225.2170 Evaluate side-chains 149 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 52 THR 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 262 GLU Chi-restraints excluded: chain R residue 320 ASN 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: 2.9990 chunk 66 optimal weight: 0.4980 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.0370 chunk 24 optimal weight: 3.9990 overall best weight: 0.9064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8294 Z= 0.230 Angle : 0.607 13.148 11238 Z= 0.313 Chirality : 0.043 0.185 1267 Planarity : 0.005 0.069 1424 Dihedral : 4.101 20.810 1124 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.13 % Allowed : 21.44 % 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: 1.71 (0.27), residues: 1014 helix: 3.26 (0.26), residues: 372 sheet: 0.08 (0.32), residues: 234 loop : -0.23 (0.32), residues: 408 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 0.012 0.001 PHE A 212 TYR 0.021 0.001 TYR R 269 ARG 0.015 0.001 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 155 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7932 (tt0) REVERT: B 175 GLN cc_start: 0.8298 (pp30) cc_final: 0.7756 (pp30) REVERT: B 325 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8174 (tpt) REVERT: G 21 MET cc_start: 0.6790 (ttp) cc_final: 0.6278 (tmt) REVERT: N 87 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8506 (mtpm) REVERT: N 125 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8773 (p) REVERT: R 138 GLU cc_start: 0.7818 (pm20) cc_final: 0.7575 (pm20) REVERT: R 139 GLU cc_start: 0.7680 (pm20) cc_final: 0.7111 (pm20) REVERT: R 197 LYS cc_start: 0.8922 (tmtm) cc_final: 0.8579 (tmmm) REVERT: R 262 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7272 (pm20) outliers start: 27 outliers final: 21 residues processed: 147 average time/residue: 1.3344 time to fit residues: 207.2355 Evaluate side-chains 149 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 52 THR 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 120 GLN 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 308 ILE Chi-restraints excluded: chain R residue 320 ASN 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: 3.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.122990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.086285 restraints weight = 12050.527| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.96 r_work: 0.2954 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8294 Z= 0.300 Angle : 0.640 13.666 11238 Z= 0.332 Chirality : 0.044 0.198 1267 Planarity : 0.005 0.058 1424 Dihedral : 4.248 21.751 1124 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.36 % Allowed : 21.55 % Favored : 75.09 % 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: 1.53 (0.27), residues: 1014 helix: 3.06 (0.26), residues: 377 sheet: 0.06 (0.32), residues: 234 loop : -0.37 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 420 HIS 0.006 0.001 HIS R 363 PHE 0.014 0.002 PHE R 169 TYR 0.020 0.002 TYR R 269 ARG 0.014 0.001 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3872.16 seconds wall clock time: 69 minutes 52.10 seconds (4192.10 seconds total)