Starting phenix.real_space_refine on Wed Feb 12 17:20:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wg7_37504/02_2025/8wg7_37504.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wg7_37504/02_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_37504/02_2025/8wg7_37504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wg7_37504/02_2025/8wg7_37504.map" model { file = "/net/cci-nas-00/data/ceres_data/8wg7_37504/02_2025/8wg7_37504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wg7_37504/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8123 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1928 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2205 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 5.33, per 1000 atoms: 0.66 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: 1.99 Conformation dependent library (CDL) restraints added in 1.1 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: 0.96 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: 2.46 Time building geometry restraints manager: 2.36 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.340 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.810 ------------------------------------------------------------------------------- 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 : 0.903 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: 1.4708 time to fit residues: 270.3957 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 : 1.000 ------------------------------------------------------------------------------- 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 = 0.127359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.090991 restraints weight = 12002.008| |-----------------------------------------------------------------------------| 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 : 0.935 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: 0.5777 (ttp) cc_final: 0.5443 (tmt) REVERT: N 31 ASN cc_start: 0.8408 (m-40) cc_final: 0.8118 (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: 1.3846 time to fit residues: 228.2287 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 : 1.001 ------------------------------------------------------------------------------- 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: 0.5980 chunk 93 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.125632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.089121 restraints weight = 12309.453| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.97 r_work: 0.3010 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8294 Z= 0.211 Angle : 0.542 7.689 11238 Z= 0.292 Chirality : 0.042 0.132 1267 Planarity : 0.004 0.050 1424 Dihedral : 4.016 19.835 1124 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.90 % Allowed : 15.64 % Favored : 81.46 % 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: 3.04 (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 0.016 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 169 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7326 (pm20) cc_final: 0.6943 (pm20) REVERT: B 175 GLN cc_start: 0.8186 (pp30) cc_final: 0.7802 (pp30) REVERT: B 217 MET cc_start: 0.8447 (ptt) cc_final: 0.8131 (pp-130) REVERT: G 21 MET cc_start: 0.5824 (ttp) cc_final: 0.5423 (tmt) REVERT: N 31 ASN cc_start: 0.8376 (m-40) cc_final: 0.8127 (m-40) REVERT: N 53 GLN cc_start: 0.8222 (mp10) cc_final: 0.7937 (mp10) REVERT: N 87 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8037 (mtpm) REVERT: N 104 THR cc_start: 0.8663 (t) cc_final: 0.8436 (t) REVERT: N 105 ARG cc_start: 0.8400 (ttp-110) cc_final: 0.8134 (ttp-110) REVERT: N 106 ASP cc_start: 0.8886 (p0) cc_final: 0.8511 (p0) REVERT: R 139 GLU cc_start: 0.7814 (pm20) cc_final: 0.7434 (pm20) REVERT: R 197 LYS cc_start: 0.8756 (tmtm) cc_final: 0.8491 (tmmm) REVERT: R 262 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: R 306 TRP cc_start: 0.8275 (t60) cc_final: 0.7934 (t-100) REVERT: R 387 GLU cc_start: 0.7186 (tp30) cc_final: 0.6932 (tp30) REVERT: R 418 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8194 (mm-30) outliers start: 25 outliers final: 12 residues processed: 157 average time/residue: 1.3368 time to fit residues: 221.8724 Evaluate side-chains 148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 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: 0.9990 chunk 63 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 R 320 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.123004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.086262 restraints weight = 12185.248| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.95 r_work: 0.2952 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8294 Z= 0.307 Angle : 0.575 7.080 11238 Z= 0.312 Chirality : 0.044 0.150 1267 Planarity : 0.005 0.050 1424 Dihedral : 4.191 21.701 1124 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.94 % Allowed : 16.57 % Favored : 79.49 % 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: 1.49 (0.27), residues: 1014 helix: 2.83 (0.26), residues: 384 sheet: 0.17 (0.32), residues: 237 loop : -0.32 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 420 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.002 PHE R 169 TYR 0.019 0.002 TYR R 148 ARG 0.007 0.001 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 166 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9203 (mt) REVERT: B 175 GLN cc_start: 0.8273 (pp30) cc_final: 0.7786 (pp30) REVERT: B 217 MET cc_start: 0.8431 (ptt) cc_final: 0.8035 (pp-130) REVERT: G 21 MET cc_start: 0.6096 (ttp) cc_final: 0.5627 (tmt) REVERT: N 31 ASN cc_start: 0.8563 (m-40) cc_final: 0.8350 (m110) REVERT: N 53 GLN cc_start: 0.8268 (mp10) cc_final: 0.7978 (mp10) REVERT: N 87 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8067 (mtpm) REVERT: N 105 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.8139 (ttp-110) REVERT: N 106 ASP cc_start: 0.8796 (p0) cc_final: 0.8534 (OUTLIER) REVERT: R 139 GLU cc_start: 0.7774 (pm20) cc_final: 0.7374 (pm20) REVERT: R 197 LYS cc_start: 0.8779 (tmtm) cc_final: 0.8471 (tmmm) REVERT: R 262 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: R 306 TRP cc_start: 0.8276 (t60) cc_final: 0.7898 (t-100) REVERT: R 387 GLU cc_start: 0.7193 (tp30) cc_final: 0.6941 (tp30) REVERT: R 418 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8164 (mm-30) outliers start: 34 outliers final: 18 residues processed: 153 average time/residue: 1.2785 time to fit residues: 207.0055 Evaluate side-chains 146 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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: 6.9990 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.124480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.087988 restraints weight = 12042.549| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.94 r_work: 0.2987 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2021 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= 0.218 Angle : 0.551 8.349 11238 Z= 0.296 Chirality : 0.042 0.133 1267 Planarity : 0.004 0.048 1424 Dihedral : 4.097 21.413 1124 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.36 % Allowed : 18.77 % Favored : 77.87 % 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: 1.61 (0.27), residues: 1014 helix: 3.09 (0.26), residues: 372 sheet: 0.09 (0.32), residues: 237 loop : -0.23 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 420 HIS 0.003 0.001 HIS A 357 PHE 0.021 0.001 PHE R 169 TYR 0.015 0.001 TYR R 148 ARG 0.006 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: 29 poor density : 138 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.9430 (mp) cc_final: 0.9199 (mt) REVERT: B 175 GLN cc_start: 0.8242 (pp30) cc_final: 0.7716 (pp30) REVERT: B 243 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8051 (p) REVERT: G 21 MET cc_start: 0.6132 (ttp) cc_final: 0.5813 (tmt) REVERT: G 58 GLU cc_start: 0.7641 (pm20) cc_final: 0.7435 (pm20) REVERT: N 31 ASN cc_start: 0.8501 (m-40) cc_final: 0.8215 (m110) REVERT: N 53 GLN cc_start: 0.8201 (mp10) cc_final: 0.7910 (mp10) REVERT: N 87 LYS cc_start: 0.8471 (mtpt) cc_final: 0.8098 (mtpm) REVERT: N 105 ARG cc_start: 0.8423 (ttp-110) cc_final: 0.8136 (ttp-110) REVERT: N 106 ASP cc_start: 0.8682 (p0) cc_final: 0.8427 (p0) REVERT: R 139 GLU cc_start: 0.7840 (pm20) cc_final: 0.7485 (pm20) REVERT: R 197 LYS cc_start: 0.8786 (tmtm) cc_final: 0.8468 (tmmm) REVERT: R 306 TRP cc_start: 0.8281 (t60) cc_final: 0.7876 (t-100) REVERT: R 418 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8101 (mm-30) outliers start: 29 outliers final: 18 residues processed: 157 average time/residue: 1.3170 time to fit residues: 218.7322 Evaluate side-chains 150 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 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 365 VAL 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: 0.9990 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 62 optimal weight: 0.0970 chunk 7 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.125483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.089093 restraints weight = 12111.911| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.94 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: 0.7532 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8294 Z= 0.181 Angle : 0.543 9.017 11238 Z= 0.290 Chirality : 0.042 0.139 1267 Planarity : 0.004 0.047 1424 Dihedral : 4.022 21.159 1124 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.82 % Allowed : 19.58 % Favored : 76.59 % 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: 3.18 (0.26), residues: 372 sheet: 0.00 (0.32), residues: 242 loop : -0.16 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 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 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 172 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8242 (pp30) cc_final: 0.7664 (pp30) REVERT: B 217 MET cc_start: 0.8352 (ptm) cc_final: 0.8002 (pp-130) REVERT: B 243 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8017 (p) REVERT: G 21 MET cc_start: 0.6061 (ttp) cc_final: 0.5649 (tmt) REVERT: G 58 GLU cc_start: 0.7720 (pm20) cc_final: 0.7501 (pm20) REVERT: N 31 ASN cc_start: 0.8423 (m-40) cc_final: 0.8130 (m-40) REVERT: N 34 MET cc_start: 0.8534 (mmm) cc_final: 0.8313 (mmm) REVERT: N 53 GLN cc_start: 0.8201 (mp10) cc_final: 0.7888 (mp10) REVERT: N 87 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8105 (mtpm) REVERT: N 105 ARG cc_start: 0.8442 (ttp-110) cc_final: 0.8139 (ttp-110) REVERT: N 106 ASP cc_start: 0.8708 (p0) cc_final: 0.8467 (p0) REVERT: R 138 GLU cc_start: 0.7917 (pm20) cc_final: 0.7692 (pm20) REVERT: R 139 GLU cc_start: 0.7876 (pm20) cc_final: 0.7548 (pm20) REVERT: R 197 LYS cc_start: 0.8782 (tmtm) cc_final: 0.8473 (tmmm) REVERT: R 306 TRP cc_start: 0.8294 (t60) cc_final: 0.7894 (t-100) REVERT: R 418 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8132 (mm-30) outliers start: 33 outliers final: 16 residues processed: 158 average time/residue: 1.3297 time to fit residues: 222.4093 Evaluate side-chains 150 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 4 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3681 r_free = 0.3681 target = 0.125527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.089137 restraints weight = 12073.184| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.95 r_work: 0.3008 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2137 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= 0.187 Angle : 0.556 9.194 11238 Z= 0.295 Chirality : 0.042 0.153 1267 Planarity : 0.004 0.057 1424 Dihedral : 3.970 20.947 1124 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.90 % Allowed : 20.74 % Favored : 76.36 % 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: 1.67 (0.27), residues: 1014 helix: 3.20 (0.26), residues: 372 sheet: -0.00 (0.32), residues: 242 loop : -0.16 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 420 HIS 0.005 0.001 HIS R 363 PHE 0.012 0.001 PHE A 212 TYR 0.014 0.001 TYR R 148 ARG 0.013 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8677 (p90) cc_final: 0.8477 (p90) REVERT: B 175 GLN cc_start: 0.8231 (pp30) cc_final: 0.7724 (pp30) REVERT: B 217 MET cc_start: 0.8361 (ptm) cc_final: 0.7964 (pp-130) REVERT: B 243 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8006 (p) REVERT: G 21 MET cc_start: 0.6014 (ttp) cc_final: 0.5575 (tmt) REVERT: G 58 GLU cc_start: 0.7742 (pm20) cc_final: 0.7483 (pm20) REVERT: N 31 ASN cc_start: 0.8427 (m-40) cc_final: 0.8153 (m-40) REVERT: N 53 GLN cc_start: 0.8211 (mp10) cc_final: 0.7880 (mp10) REVERT: N 87 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8044 (mtpm) REVERT: N 105 ARG cc_start: 0.8440 (ttp-110) cc_final: 0.8139 (ttp-110) REVERT: N 106 ASP cc_start: 0.8800 (p0) cc_final: 0.8587 (p0) REVERT: N 125 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8641 (p) REVERT: R 138 GLU cc_start: 0.7886 (pm20) cc_final: 0.7613 (pm20) REVERT: R 139 GLU cc_start: 0.7934 (pm20) cc_final: 0.7539 (pm20) REVERT: R 197 LYS cc_start: 0.8823 (tmtm) cc_final: 0.8504 (tmmm) REVERT: R 306 TRP cc_start: 0.8265 (t60) cc_final: 0.7947 (t-100) REVERT: R 418 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8127 (mm-30) outliers start: 25 outliers final: 16 residues processed: 156 average time/residue: 1.2935 time to fit residues: 213.4034 Evaluate side-chains 152 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN A 64 HIS 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 = 0.3676 r_free = 0.3676 target = 0.124914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.088283 restraints weight = 12179.869| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.97 r_work: 0.2987 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2204 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= 0.220 Angle : 0.583 13.414 11238 Z= 0.304 Chirality : 0.042 0.157 1267 Planarity : 0.004 0.058 1424 Dihedral : 4.005 20.905 1124 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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: 1.64 (0.27), residues: 1014 helix: 3.18 (0.26), residues: 372 sheet: -0.02 (0.32), residues: 242 loop : -0.20 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 420 HIS 0.005 0.001 HIS R 363 PHE 0.012 0.001 PHE R 169 TYR 0.014 0.001 TYR N 32 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 160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8252 (pp30) cc_final: 0.7649 (pp30) REVERT: B 217 MET cc_start: 0.8373 (ptm) cc_final: 0.7996 (pp-130) REVERT: B 243 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8048 (p) REVERT: G 21 MET cc_start: 0.5984 (ttp) cc_final: 0.5546 (tmt) REVERT: G 58 GLU cc_start: 0.7793 (pm20) cc_final: 0.7527 (pm20) REVERT: N 31 ASN cc_start: 0.8487 (m-40) cc_final: 0.8199 (m110) REVERT: N 53 GLN cc_start: 0.8225 (mp10) cc_final: 0.7895 (mp10) REVERT: N 87 LYS cc_start: 0.8431 (mtpt) cc_final: 0.7981 (mtpm) REVERT: N 105 ARG cc_start: 0.8452 (ttp-110) cc_final: 0.8151 (ttp-110) REVERT: N 106 ASP cc_start: 0.8790 (p0) cc_final: 0.8562 (p0) REVERT: N 125 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8631 (p) REVERT: R 138 GLU cc_start: 0.7870 (pm20) cc_final: 0.7595 (pm20) REVERT: R 139 GLU cc_start: 0.7944 (pm20) cc_final: 0.7557 (pm20) REVERT: R 197 LYS cc_start: 0.8812 (tmtm) cc_final: 0.8486 (tmmm) REVERT: R 262 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7437 (pm20) REVERT: R 306 TRP cc_start: 0.8252 (t60) cc_final: 0.7928 (t-100) REVERT: R 418 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8122 (mm-30) outliers start: 26 outliers final: 16 residues processed: 151 average time/residue: 1.3133 time to fit residues: 209.5948 Evaluate side-chains 153 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN N 39 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.125108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.088554 restraints weight = 12212.238| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.98 r_work: 0.2995 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2227 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= 0.200 Angle : 0.580 14.041 11238 Z= 0.301 Chirality : 0.042 0.196 1267 Planarity : 0.004 0.064 1424 Dihedral : 3.991 20.669 1124 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.90 % Allowed : 21.21 % 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: 1.66 (0.27), residues: 1014 helix: 3.23 (0.26), residues: 372 sheet: -0.02 (0.32), residues: 242 loop : -0.21 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 420 HIS 0.005 0.001 HIS R 363 PHE 0.012 0.001 PHE A 212 TYR 0.013 0.001 TYR 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 163 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8239 (pp30) cc_final: 0.7632 (pp30) REVERT: B 217 MET cc_start: 0.8348 (ptm) cc_final: 0.7984 (pp-130) REVERT: B 243 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8035 (p) REVERT: B 262 MET cc_start: 0.7457 (tpp) cc_final: 0.7131 (tpp) REVERT: G 21 MET cc_start: 0.6007 (ttp) cc_final: 0.5565 (tmt) REVERT: G 58 GLU cc_start: 0.7772 (pm20) cc_final: 0.7523 (pm20) REVERT: N 31 ASN cc_start: 0.8481 (m-40) cc_final: 0.8179 (m-40) REVERT: N 53 GLN cc_start: 0.8224 (mp10) cc_final: 0.7894 (mp10) REVERT: N 87 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8042 (mtpm) REVERT: N 105 ARG cc_start: 0.8453 (ttp-110) cc_final: 0.8175 (ttp-110) REVERT: N 106 ASP cc_start: 0.8802 (p0) cc_final: 0.8582 (OUTLIER) REVERT: N 125 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8643 (p) REVERT: R 138 GLU cc_start: 0.7821 (pm20) cc_final: 0.7539 (pm20) REVERT: R 139 GLU cc_start: 0.7903 (pm20) cc_final: 0.7466 (pm20) REVERT: R 197 LYS cc_start: 0.8829 (tmtm) cc_final: 0.8503 (tmmm) REVERT: R 262 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7418 (pm20) REVERT: R 292 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8118 (tp30) REVERT: R 306 TRP cc_start: 0.8244 (t60) cc_final: 0.7938 (t-100) REVERT: R 418 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8187 (mm-30) outliers start: 25 outliers final: 18 residues processed: 153 average time/residue: 1.3205 time to fit residues: 213.3162 Evaluate side-chains 155 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 110 ASN N 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.125807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.089446 restraints weight = 12167.797| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.97 r_work: 0.3005 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8294 Z= 0.185 Angle : 0.586 13.328 11238 Z= 0.304 Chirality : 0.042 0.191 1267 Planarity : 0.004 0.045 1424 Dihedral : 3.976 20.514 1124 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.55 % Allowed : 22.02 % 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: 1.68 (0.27), residues: 1014 helix: 3.23 (0.26), residues: 372 sheet: -0.02 (0.32), residues: 242 loop : -0.19 (0.33), residues: 400 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 0.011 0.001 PHE A 212 TYR 0.014 0.001 TYR A 253 ARG 0.009 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8214 (pp30) cc_final: 0.7694 (pp30) REVERT: B 217 MET cc_start: 0.8347 (ptm) cc_final: 0.7995 (pp-130) REVERT: B 243 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.7991 (p) REVERT: B 262 MET cc_start: 0.7404 (tpp) cc_final: 0.7163 (tpp) REVERT: G 21 MET cc_start: 0.5984 (ttp) cc_final: 0.5538 (tmt) REVERT: G 58 GLU cc_start: 0.7780 (pm20) cc_final: 0.7535 (pm20) REVERT: N 31 ASN cc_start: 0.8462 (m-40) cc_final: 0.8154 (m-40) REVERT: N 53 GLN cc_start: 0.8229 (mp10) cc_final: 0.7890 (mp10) REVERT: N 87 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8041 (mtpm) REVERT: N 105 ARG cc_start: 0.8444 (ttp-110) cc_final: 0.8143 (ttp-110) REVERT: N 106 ASP cc_start: 0.8816 (p0) cc_final: 0.8595 (OUTLIER) REVERT: N 125 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8633 (p) REVERT: R 138 GLU cc_start: 0.7837 (pm20) cc_final: 0.7559 (pm20) REVERT: R 139 GLU cc_start: 0.7898 (pm20) cc_final: 0.7459 (pm20) REVERT: R 197 LYS cc_start: 0.8815 (tmtm) cc_final: 0.8508 (tmmm) REVERT: R 262 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7418 (pm20) REVERT: R 292 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8071 (tp30) REVERT: R 306 TRP cc_start: 0.8218 (t60) cc_final: 0.7929 (t-100) REVERT: R 418 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8112 (mm-30) outliers start: 22 outliers final: 14 residues processed: 152 average time/residue: 1.3001 time to fit residues: 209.0536 Evaluate side-chains 150 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 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 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 365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN A 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 = 0.3681 r_free = 0.3681 target = 0.125206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.088557 restraints weight = 12283.901| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.99 r_work: 0.2994 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8294 Z= 0.216 Angle : 0.590 13.685 11238 Z= 0.308 Chirality : 0.043 0.196 1267 Planarity : 0.004 0.047 1424 Dihedral : 4.002 20.666 1124 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.32 % Allowed : 22.36 % Favored : 75.32 % 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: 3.20 (0.26), residues: 372 sheet: 0.00 (0.32), residues: 242 loop : -0.20 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 420 HIS 0.005 0.001 HIS R 363 PHE 0.011 0.001 PHE A 212 TYR 0.014 0.001 TYR A 311 ARG 0.011 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6619.88 seconds wall clock time: 117 minutes 31.47 seconds (7051.47 seconds total)