Starting phenix.real_space_refine on Wed Mar 12 17:52:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wg7_37504/03_2025/8wg7_37504.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wg7_37504/03_2025/8wg7_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/cci-nas-00/data/ceres_data/8wg7_37504/03_2025/8wg7_37504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wg7_37504/03_2025/8wg7_37504.map" model { file = "/net/cci-nas-00/data/ceres_data/8wg7_37504/03_2025/8wg7_37504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wg7_37504/03_2025/8wg7_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. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.92, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.2 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: 0.86 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: 3.04 Time building geometry restraints manager: 2.23 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: 0.00 - 1.29: 10815 1.29 - 2.57: 353 2.57 - 3.86: 58 3.86 - 5.15: 10 5.15 - 6.43: 2 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.860 Find NCS groups from input model: 0.090 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:17.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.730 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.859 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: 1.4400 time to fit residues: 264.7701 Evaluate side-chains 137 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.127362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.090997 restraints weight = 12001.458| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.94 r_work: 0.3040 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8156 (tt0) REVERT: B 175 GLN cc_start: 0.8128 (pp30) cc_final: 0.7808 (pp30) REVERT: B 217 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8165 (pp-130) REVERT: G 21 MET cc_start: 0.5781 (ttp) cc_final: 0.5446 (tmt) REVERT: N 31 ASN cc_start: 0.8408 (m-40) cc_final: 0.8117 (m110) REVERT: N 53 GLN cc_start: 0.8172 (mp10) cc_final: 0.7878 (mp10) REVERT: N 87 LYS cc_start: 0.8564 (mtpt) cc_final: 0.8267 (mtpm) REVERT: N 104 THR cc_start: 0.8461 (t) cc_final: 0.8179 (t) REVERT: N 106 ASP cc_start: 0.8859 (p0) cc_final: 0.8306 (p0) REVERT: R 139 GLU cc_start: 0.7753 (pm20) cc_final: 0.7305 (pm20) REVERT: R 306 TRP cc_start: 0.8271 (t60) cc_final: 0.7912 (t-100) REVERT: R 418 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8235 (mm-30) outliers start: 20 outliers final: 6 residues processed: 156 average time/residue: 1.4727 time to fit residues: 242.7594 Evaluate side-chains 144 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 217 MET 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 77 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.125183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.088547 restraints weight = 12310.520| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.96 r_work: 0.3002 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8294 Z= 0.230 Angle : 0.547 7.104 11238 Z= 0.296 Chirality : 0.042 0.132 1267 Planarity : 0.004 0.050 1424 Dihedral : 4.038 20.017 1124 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.13 % Allowed : 15.53 % Favored : 81.34 % 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: 3.04 (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 0.020 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 170 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7329 (pm20) cc_final: 0.6953 (pm20) REVERT: A 283 ARG cc_start: 0.7592 (mtm110) cc_final: 0.7386 (mtp-110) REVERT: B 175 GLN cc_start: 0.8198 (pp30) cc_final: 0.7770 (pp30) REVERT: B 217 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8149 (pp-130) REVERT: G 21 MET cc_start: 0.5830 (ttp) cc_final: 0.5428 (tmt) REVERT: N 31 ASN cc_start: 0.8407 (m-40) cc_final: 0.8138 (m-40) REVERT: N 53 GLN cc_start: 0.8221 (mp10) cc_final: 0.7940 (mp10) REVERT: N 87 LYS cc_start: 0.8474 (mtpt) cc_final: 0.8202 (mtpm) REVERT: N 104 THR cc_start: 0.8672 (t) cc_final: 0.8444 (t) REVERT: N 105 ARG cc_start: 0.8401 (ttp-110) cc_final: 0.8130 (ttp-110) REVERT: N 106 ASP cc_start: 0.8884 (p0) cc_final: 0.8507 (p0) REVERT: R 139 GLU cc_start: 0.7744 (pm20) cc_final: 0.7330 (pm20) REVERT: R 197 LYS cc_start: 0.8759 (tmtm) cc_final: 0.8498 (tmmm) REVERT: R 262 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: R 306 TRP cc_start: 0.8279 (t60) cc_final: 0.7933 (t-100) REVERT: R 387 GLU cc_start: 0.7309 (tp30) cc_final: 0.7070 (tp30) REVERT: R 418 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8180 (mm-30) outliers start: 27 outliers final: 12 residues processed: 158 average time/residue: 1.3140 time to fit residues: 220.3684 Evaluate side-chains 148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 217 MET 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 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 13 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.124407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.087603 restraints weight = 12152.702| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.97 r_work: 0.2986 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8294 Z= 0.246 Angle : 0.548 7.589 11238 Z= 0.296 Chirality : 0.043 0.132 1267 Planarity : 0.004 0.049 1424 Dihedral : 4.090 20.851 1124 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.71 % Allowed : 16.69 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.27), residues: 1014 helix: 2.96 (0.26), residues: 378 sheet: 0.15 (0.32), residues: 242 loop : -0.20 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 420 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.001 PHE R 169 TYR 0.018 0.001 TYR R 148 ARG 0.008 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 172 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9219 (mt) REVERT: A 283 ARG cc_start: 0.7718 (mtm110) cc_final: 0.7483 (mtp-110) REVERT: A 386 MET cc_start: 0.8812 (ttp) cc_final: 0.8577 (ttp) REVERT: B 175 GLN cc_start: 0.8251 (pp30) cc_final: 0.7768 (pp30) REVERT: B 217 MET cc_start: 0.8425 (ptt) cc_final: 0.8060 (pp-130) REVERT: G 21 MET cc_start: 0.5886 (ttp) cc_final: 0.5440 (tmt) REVERT: N 31 ASN cc_start: 0.8485 (m-40) cc_final: 0.8194 (m110) REVERT: N 53 GLN cc_start: 0.8238 (mp10) cc_final: 0.7937 (mp10) REVERT: N 87 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8185 (mtpm) REVERT: N 105 ARG cc_start: 0.8408 (ttp-110) cc_final: 0.8114 (ttp-110) REVERT: N 106 ASP cc_start: 0.8858 (p0) cc_final: 0.8576 (OUTLIER) REVERT: R 139 GLU cc_start: 0.7813 (pm20) cc_final: 0.7406 (pm20) REVERT: R 197 LYS cc_start: 0.8786 (tmtm) cc_final: 0.8473 (tmmm) REVERT: R 262 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: R 306 TRP cc_start: 0.8287 (t60) cc_final: 0.7906 (t-100) REVERT: R 387 GLU cc_start: 0.7268 (tp30) cc_final: 0.7030 (tp30) REVERT: R 418 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8125 (mm-30) outliers start: 32 outliers final: 18 residues processed: 160 average time/residue: 1.5577 time to fit residues: 263.0377 Evaluate side-chains 148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 LEU 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 G residue 30 VAL 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 365 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 95 optimal weight: 0.0010 chunk 90 optimal weight: 1.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.125996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.089583 restraints weight = 12032.675| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.95 r_work: 0.3006 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8294 Z= 0.177 Angle : 0.538 7.929 11238 Z= 0.288 Chirality : 0.042 0.131 1267 Planarity : 0.004 0.048 1424 Dihedral : 4.005 20.343 1124 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.01 % Allowed : 18.89 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.27), residues: 1014 helix: 3.14 (0.26), residues: 372 sheet: 0.09 (0.32), residues: 242 loop : -0.17 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 420 HIS 0.003 0.001 HIS A 357 PHE 0.018 0.001 PHE R 169 TYR 0.014 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 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ARG cc_start: 0.7650 (mtm110) cc_final: 0.7425 (mtp-110) REVERT: A 386 MET cc_start: 0.8801 (ttp) cc_final: 0.8579 (ttp) REVERT: B 175 GLN cc_start: 0.8216 (pp30) cc_final: 0.7761 (pp30) REVERT: B 243 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8033 (p) REVERT: G 21 MET cc_start: 0.5864 (ttp) cc_final: 0.5429 (tmt) REVERT: N 31 ASN cc_start: 0.8374 (m-40) cc_final: 0.8108 (m-40) REVERT: N 53 GLN cc_start: 0.8180 (mp10) cc_final: 0.7873 (mp10) REVERT: N 87 LYS cc_start: 0.8434 (mtpt) cc_final: 0.8226 (mtpm) REVERT: N 105 ARG cc_start: 0.8414 (ttp-110) cc_final: 0.8114 (ttp-110) REVERT: N 106 ASP cc_start: 0.8742 (p0) cc_final: 0.8488 (p0) REVERT: R 139 GLU cc_start: 0.7830 (pm20) cc_final: 0.7491 (pm20) REVERT: R 197 LYS cc_start: 0.8766 (tmtm) cc_final: 0.8456 (tmmm) REVERT: R 306 TRP cc_start: 0.8244 (t60) cc_final: 0.7876 (t-100) REVERT: R 418 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8116 (mm-30) outliers start: 26 outliers final: 16 residues processed: 157 average time/residue: 1.2801 time to fit residues: 212.8451 Evaluate side-chains 151 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 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 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 365 VAL Chi-restraints excluded: chain R residue 397 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 71 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 62 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.126100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.089647 restraints weight = 12130.204| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.96 r_work: 0.3008 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8294 Z= 0.181 Angle : 0.547 8.762 11238 Z= 0.291 Chirality : 0.041 0.141 1267 Planarity : 0.004 0.051 1424 Dihedral : 3.967 20.485 1124 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.59 % Allowed : 19.00 % 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: 1.71 (0.27), residues: 1014 helix: 3.20 (0.26), residues: 372 sheet: 0.10 (0.32), residues: 241 loop : -0.16 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 420 HIS 0.004 0.001 HIS R 363 PHE 0.014 0.001 PHE R 169 TYR 0.014 0.001 TYR R 148 ARG 0.011 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 174 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ARG cc_start: 0.7681 (mtm110) cc_final: 0.7445 (mtp-110) REVERT: A 386 MET cc_start: 0.8779 (ttp) cc_final: 0.8528 (ttp) REVERT: B 175 GLN cc_start: 0.8206 (pp30) cc_final: 0.7728 (pp30) REVERT: B 217 MET cc_start: 0.8484 (ptt) cc_final: 0.8070 (pp-130) REVERT: B 243 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.8028 (p) REVERT: G 21 MET cc_start: 0.5855 (ttp) cc_final: 0.5483 (tmt) REVERT: N 31 ASN cc_start: 0.8370 (m-40) cc_final: 0.8102 (m-40) REVERT: N 53 GLN cc_start: 0.8241 (mp10) cc_final: 0.7922 (mp10) REVERT: N 87 LYS cc_start: 0.8420 (mtpt) cc_final: 0.8198 (mtpm) REVERT: N 104 THR cc_start: 0.8776 (t) cc_final: 0.8505 (t) REVERT: N 105 ARG cc_start: 0.8443 (ttp-110) cc_final: 0.8135 (ttp-110) REVERT: N 106 ASP cc_start: 0.8728 (p0) cc_final: 0.8420 (p0) REVERT: R 138 GLU cc_start: 0.7878 (pm20) cc_final: 0.7649 (pm20) REVERT: R 139 GLU cc_start: 0.7852 (pm20) cc_final: 0.7495 (pm20) REVERT: R 197 LYS cc_start: 0.8757 (tmtm) cc_final: 0.8475 (tmmm) REVERT: R 306 TRP cc_start: 0.8262 (t60) cc_final: 0.7881 (t-100) REVERT: R 418 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8111 (mm-30) outliers start: 31 outliers final: 19 residues processed: 159 average time/residue: 1.2335 time to fit residues: 207.4858 Evaluate side-chains 156 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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 90 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.125714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.089230 restraints weight = 12094.182| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.95 r_work: 0.3001 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2070 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= 0.201 Angle : 0.562 9.015 11238 Z= 0.298 Chirality : 0.042 0.150 1267 Planarity : 0.004 0.055 1424 Dihedral : 3.987 20.536 1124 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.48 % Allowed : 19.81 % 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: 1.69 (0.27), residues: 1014 helix: 3.22 (0.26), residues: 372 sheet: 0.06 (0.32), residues: 242 loop : -0.20 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 420 HIS 0.005 0.001 HIS R 363 PHE 0.013 0.001 PHE R 169 TYR 0.014 0.001 TYR R 148 ARG 0.012 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 174 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7940 (mm110) REVERT: A 35 GLN cc_start: 0.8732 (tt0) cc_final: 0.7994 (mp10) REVERT: A 283 ARG cc_start: 0.7677 (mtm110) cc_final: 0.7430 (mtp-110) REVERT: A 386 MET cc_start: 0.8780 (ttp) cc_final: 0.8548 (ttp) REVERT: B 175 GLN cc_start: 0.8215 (pp30) cc_final: 0.7720 (pp30) REVERT: B 217 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8019 (pp-130) REVERT: B 243 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8041 (p) REVERT: G 21 MET cc_start: 0.5823 (ttp) cc_final: 0.5438 (tmt) REVERT: N 31 ASN cc_start: 0.8414 (m-40) cc_final: 0.8142 (m-40) REVERT: N 53 GLN cc_start: 0.8247 (mp10) cc_final: 0.7921 (mp10) REVERT: N 87 LYS cc_start: 0.8411 (mtpt) cc_final: 0.7988 (mtpm) REVERT: N 104 THR cc_start: 0.8805 (t) cc_final: 0.8529 (t) REVERT: N 105 ARG cc_start: 0.8450 (ttp-110) cc_final: 0.8141 (ttp-110) REVERT: N 106 ASP cc_start: 0.8798 (p0) cc_final: 0.8534 (p0) REVERT: R 138 GLU cc_start: 0.7878 (pm20) cc_final: 0.7644 (pm20) REVERT: R 139 GLU cc_start: 0.7873 (pm20) cc_final: 0.7489 (pm20) REVERT: R 197 LYS cc_start: 0.8782 (tmtm) cc_final: 0.8475 (tmmm) REVERT: R 306 TRP cc_start: 0.8267 (t60) cc_final: 0.7895 (t-100) REVERT: R 418 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8122 (mm-30) outliers start: 30 outliers final: 16 residues processed: 162 average time/residue: 1.3131 time to fit residues: 225.3023 Evaluate side-chains 154 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 217 MET 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 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 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 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 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 64 HIS A 390 GLN N 39 GLN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.125229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.089001 restraints weight = 12200.564| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.95 r_work: 0.3002 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8294 Z= 0.215 Angle : 0.589 12.538 11238 Z= 0.307 Chirality : 0.042 0.157 1267 Planarity : 0.004 0.060 1424 Dihedral : 4.002 20.737 1124 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.01 % Allowed : 21.21 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.27), residues: 1014 helix: 3.19 (0.26), residues: 372 sheet: 0.05 (0.32), residues: 242 loop : -0.20 (0.33), residues: 400 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 R 367 TYR 0.014 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 165 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ARG cc_start: 0.7751 (mtm110) cc_final: 0.7487 (mtp-110) REVERT: A 386 MET cc_start: 0.8788 (ttp) cc_final: 0.8553 (ttp) REVERT: B 175 GLN cc_start: 0.8233 (pp30) cc_final: 0.7642 (pp30) REVERT: B 217 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7993 (pp-130) REVERT: B 243 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8043 (p) REVERT: G 21 MET cc_start: 0.5856 (ttp) cc_final: 0.5463 (tmt) REVERT: N 31 ASN cc_start: 0.8457 (m-40) cc_final: 0.8156 (m-40) REVERT: N 53 GLN cc_start: 0.8263 (mp10) cc_final: 0.7936 (mp10) REVERT: N 87 LYS cc_start: 0.8460 (mtpt) cc_final: 0.8016 (mtpm) REVERT: N 105 ARG cc_start: 0.8369 (ttp-110) cc_final: 0.8054 (ttp-110) REVERT: N 106 ASP cc_start: 0.8793 (p0) cc_final: 0.8573 (OUTLIER) REVERT: R 138 GLU cc_start: 0.7883 (pm20) cc_final: 0.7604 (pm20) REVERT: R 139 GLU cc_start: 0.7923 (pm20) cc_final: 0.7504 (pm20) REVERT: R 197 LYS cc_start: 0.8835 (tmtm) cc_final: 0.8518 (tmmm) REVERT: R 306 TRP cc_start: 0.8287 (t60) cc_final: 0.7906 (t-100) REVERT: R 418 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8124 (mm-30) outliers start: 26 outliers final: 17 residues processed: 154 average time/residue: 1.4145 time to fit residues: 230.3728 Evaluate side-chains 155 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 217 MET 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 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 365 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.123514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.086909 restraints weight = 12253.865| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.96 r_work: 0.2962 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8294 Z= 0.276 Angle : 0.617 13.293 11238 Z= 0.322 Chirality : 0.044 0.189 1267 Planarity : 0.005 0.065 1424 Dihedral : 4.115 21.249 1124 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.01 % Allowed : 21.09 % Favored : 75.90 % 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: 3.15 (0.26), residues: 371 sheet: 0.03 (0.32), residues: 242 loop : -0.20 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 420 HIS 0.005 0.001 HIS R 363 PHE 0.013 0.001 PHE R 169 TYR 0.017 0.002 TYR N 32 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 156 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 ARG cc_start: 0.8233 (mtm110) cc_final: 0.8030 (mtm-85) REVERT: A 386 MET cc_start: 0.8781 (ttp) cc_final: 0.8533 (ttp) REVERT: B 175 GLN cc_start: 0.8269 (pp30) cc_final: 0.7694 (pp30) REVERT: B 217 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7993 (pp-130) REVERT: G 21 MET cc_start: 0.6065 (ttp) cc_final: 0.5647 (tmt) REVERT: N 31 ASN cc_start: 0.8513 (m-40) cc_final: 0.8235 (m110) REVERT: N 53 GLN cc_start: 0.8212 (mp10) cc_final: 0.7891 (mp10) REVERT: N 87 LYS cc_start: 0.8380 (mtpt) cc_final: 0.7905 (mtpm) REVERT: N 105 ARG cc_start: 0.8418 (ttp-110) cc_final: 0.8143 (ttp-110) REVERT: N 106 ASP cc_start: 0.8764 (p0) cc_final: 0.8538 (OUTLIER) REVERT: R 138 GLU cc_start: 0.7837 (pm20) cc_final: 0.7595 (pm20) REVERT: R 139 GLU cc_start: 0.7894 (pm20) cc_final: 0.7444 (pm20) REVERT: R 197 LYS cc_start: 0.8841 (tmtm) cc_final: 0.8519 (tmmm) REVERT: R 418 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8174 (mm-30) outliers start: 26 outliers final: 20 residues processed: 147 average time/residue: 1.5192 time to fit residues: 235.9103 Evaluate side-chains 149 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN 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 217 MET 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 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 365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 0.0770 chunk 10 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.088563 restraints weight = 12154.352| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.95 r_work: 0.2990 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8294 Z= 0.186 Angle : 0.597 13.008 11238 Z= 0.310 Chirality : 0.043 0.190 1267 Planarity : 0.004 0.069 1424 Dihedral : 4.059 20.952 1124 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.20 % Allowed : 22.13 % Favored : 75.67 % 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: 1.67 (0.27), residues: 1014 helix: 3.22 (0.26), residues: 371 sheet: 0.08 (0.33), residues: 232 loop : -0.25 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 420 HIS 0.005 0.001 HIS R 363 PHE 0.012 0.001 PHE A 212 TYR 0.015 0.001 TYR A 311 ARG 0.015 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 158 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8058 (mt0) REVERT: A 386 MET cc_start: 0.8776 (ttp) cc_final: 0.8560 (ttp) REVERT: B 175 GLN cc_start: 0.8249 (pp30) cc_final: 0.7676 (pp30) REVERT: B 243 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8049 (p) REVERT: G 21 MET cc_start: 0.5988 (ttp) cc_final: 0.5620 (tmt) REVERT: N 31 ASN cc_start: 0.8458 (m-40) cc_final: 0.8186 (m110) REVERT: N 53 GLN cc_start: 0.8196 (mp10) cc_final: 0.7870 (mp10) REVERT: N 87 LYS cc_start: 0.8414 (mtpt) cc_final: 0.8016 (mtpm) REVERT: N 105 ARG cc_start: 0.8415 (ttp-110) cc_final: 0.8127 (ttp-110) REVERT: N 106 ASP cc_start: 0.8779 (p0) cc_final: 0.8568 (OUTLIER) REVERT: R 138 GLU cc_start: 0.7833 (pm20) cc_final: 0.7599 (pm20) REVERT: R 139 GLU cc_start: 0.7926 (pm20) cc_final: 0.7490 (pm20) REVERT: R 197 LYS cc_start: 0.8826 (tmtm) cc_final: 0.8508 (tmmm) REVERT: R 292 GLU cc_start: 0.8929 (mm-30) cc_final: 0.7990 (tp30) REVERT: R 306 TRP cc_start: 0.8307 (t60) cc_final: 0.7926 (t-100) REVERT: R 418 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8165 (mm-30) outliers start: 19 outliers final: 16 residues processed: 152 average time/residue: 1.4696 time to fit residues: 236.0424 Evaluate side-chains 152 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 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 365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.124756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.088479 restraints weight = 12266.949| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.95 r_work: 0.2988 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8294 Z= 0.218 Angle : 0.621 13.144 11238 Z= 0.322 Chirality : 0.043 0.191 1267 Planarity : 0.005 0.069 1424 Dihedral : 4.061 20.803 1124 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.55 % Allowed : 22.36 % 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: 1.66 (0.27), residues: 1014 helix: 3.21 (0.26), residues: 371 sheet: 0.01 (0.32), residues: 242 loop : -0.19 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 420 HIS 0.005 0.001 HIS R 363 PHE 0.012 0.001 PHE A 212 TYR 0.015 0.001 TYR A 253 ARG 0.016 0.001 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6905.39 seconds wall clock time: 121 minutes 55.36 seconds (7315.36 seconds total)