Starting phenix.real_space_refine on Wed Mar 12 20:21:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d3s_30566/03_2025/7d3s_30566.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d3s_30566/03_2025/7d3s_30566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d3s_30566/03_2025/7d3s_30566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d3s_30566/03_2025/7d3s_30566.map" model { file = "/net/cci-nas-00/data/ceres_data/7d3s_30566/03_2025/7d3s_30566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d3s_30566/03_2025/7d3s_30566.cif" } resolution = 2.9 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= 0.006 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 50 5.16 5 C 5286 2.51 5 N 1473 2.21 5 O 1529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8338 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2179 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 4, 'TRANS': 261} Chain breaks: 2 Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1921 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2616 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Time building chain proxies: 5.05, per 1000 atoms: 0.61 Number of scatterers: 8338 At special positions: 0 Unit cell: (122.84, 98.4936, 107.347, 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 50 16.00 O 1529 8.00 N 1473 7.00 C 5286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 215 " - pdb=" SG CYS R 285 " distance=2.02 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 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: 1.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.2% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'P' and resid 1 through 27 Processing helix chain 'R' and resid 132 through 166 Processing helix chain 'R' and resid 167 through 171 removed outlier: 3.509A pdb=" N LEU R 170 " --> pdb=" O PHE R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 200 removed outlier: 3.527A pdb=" N ILE R 177 " --> pdb=" O THR R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 246 Processing helix chain 'R' and resid 250 through 281 removed outlier: 3.832A pdb=" N GLN R 256 " --> pdb=" O ARG R 252 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY R 257 " --> pdb=" O LYS R 253 " (cutoff:3.500A) Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 291 through 327 removed outlier: 4.202A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Proline residue: R 301 - end of helix removed outlier: 3.867A pdb=" N GLN R 327 " --> pdb=" O LYS R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 346 Processing helix chain 'R' and resid 347 through 352 Processing helix chain 'R' and resid 365 through 377 Processing helix chain 'R' and resid 379 through 391 Processing helix chain 'R' and resid 392 through 405 removed outlier: 3.560A pdb=" N LYS R 402 " --> pdb=" O GLU R 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.724A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 252 through 268 removed outlier: 4.212A pdb=" N GLN A 257 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLU A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.026A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.591A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 381 Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 21 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.886A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.659A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.286A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.574A 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: 3.819A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.791A 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: 5.939A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.927A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.932A 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: 6.985A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.444A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.644A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (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 11 through 12 removed outlier: 6.898A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1284 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: 2.23 Time building geometry restraints manager: 2.31 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: 2750 1.34 - 1.46: 1906 1.46 - 1.58: 3780 1.58 - 1.70: 0 1.70 - 1.81: 71 Bond restraints: 8507 Sorted by residual: bond pdb=" CA TYR A 381 " pdb=" C TYR A 381 " ideal model delta sigma weight residual 1.523 1.490 0.033 1.41e-02 5.03e+03 5.38e+00 bond pdb=" CB TRP B 63 " pdb=" CG TRP B 63 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.72e+00 bond pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 1.498 1.462 0.036 3.10e-02 1.04e+03 1.33e+00 bond pdb=" N CYS R 389 " pdb=" CA CYS R 389 " ideal model delta sigma weight residual 1.460 1.446 0.014 1.27e-02 6.20e+03 1.21e+00 bond pdb=" CA PHE R 371 " pdb=" C PHE R 371 " ideal model delta sigma weight residual 1.525 1.510 0.015 1.37e-02 5.33e+03 1.17e+00 ... (remaining 8502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 10991 1.41 - 2.81: 448 2.81 - 4.22: 51 4.22 - 5.62: 6 5.62 - 7.03: 3 Bond angle restraints: 11499 Sorted by residual: angle pdb=" N HIS R 211 " pdb=" CA HIS R 211 " pdb=" C HIS R 211 " ideal model delta sigma weight residual 112.58 108.88 3.70 1.22e+00 6.72e-01 9.19e+00 angle pdb=" C LEU R 374 " pdb=" N ALA R 375 " pdb=" CA ALA R 375 " ideal model delta sigma weight residual 122.06 116.46 5.60 1.86e+00 2.89e-01 9.07e+00 angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 114.80 118.98 -4.18 1.42e+00 4.96e-01 8.65e+00 angle pdb=" CA TYR R 146 " pdb=" CB TYR R 146 " pdb=" CG TYR R 146 " ideal model delta sigma weight residual 113.90 118.91 -5.01 1.80e+00 3.09e-01 7.75e+00 angle pdb=" N ALA R 245 " pdb=" CA ALA R 245 " pdb=" C ALA R 245 " ideal model delta sigma weight residual 114.31 111.14 3.17 1.29e+00 6.01e-01 6.02e+00 ... (remaining 11494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4560 17.79 - 35.57: 431 35.57 - 53.36: 50 53.36 - 71.14: 17 71.14 - 88.93: 7 Dihedral angle restraints: 5065 sinusoidal: 2025 harmonic: 3040 Sorted by residual: dihedral pdb=" CA LEU B 70 " pdb=" C LEU B 70 " pdb=" N VAL B 71 " pdb=" CA VAL B 71 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA PHE R 358 " pdb=" C PHE R 358 " pdb=" N ALA R 359 " pdb=" CA ALA R 359 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 788 0.036 - 0.071: 365 0.071 - 0.107: 97 0.107 - 0.142: 26 0.142 - 0.178: 1 Chirality restraints: 1277 Sorted by residual: chirality pdb=" CA PRO N 102 " pdb=" N PRO N 102 " pdb=" C PRO N 102 " pdb=" CB PRO N 102 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1274 not shown) Planarity restraints: 1469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 372 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C PHE R 372 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE R 372 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU R 373 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 387 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LEU R 387 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU R 387 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR R 388 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 386 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.13e+00 pdb=" C VAL R 386 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL R 386 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU R 387 " -0.017 2.00e-02 2.50e+03 ... (remaining 1466 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1551 2.77 - 3.30: 7877 3.30 - 3.83: 14171 3.83 - 4.37: 17502 4.37 - 4.90: 29472 Nonbonded interactions: 70573 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.237 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.241 3.040 nonbonded pdb=" NZ LYS R 323 " pdb=" OE1 GLN A 374 " model vdw 2.266 3.120 nonbonded pdb=" NE2 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.277 3.120 nonbonded pdb=" NH1 ARG B 96 " pdb=" OE2 GLU B 138 " model vdw 2.285 3.120 ... (remaining 70568 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: 0.390 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.490 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:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8507 Z= 0.271 Angle : 0.643 7.026 11499 Z= 0.394 Chirality : 0.043 0.178 1277 Planarity : 0.005 0.058 1469 Dihedral : 13.878 88.926 3090 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % 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: -2.28 (0.23), residues: 1030 helix: -0.99 (0.23), residues: 423 sheet: -0.95 (0.32), residues: 219 loop : -2.31 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 82 HIS 0.008 0.001 HIS R 178 PHE 0.025 0.002 PHE R 313 TYR 0.016 0.002 TYR R 146 ARG 0.011 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.897 Fit side-chains REVERT: R 346 LEU cc_start: 0.8167 (mp) cc_final: 0.7678 (mt) REVERT: R 368 ILE cc_start: 0.7624 (tt) cc_final: 0.7414 (tp) REVERT: A 27 GLU cc_start: 0.6300 (tp30) cc_final: 0.5629 (tp30) REVERT: A 60 MET cc_start: 0.7722 (mmm) cc_final: 0.7407 (mmt) REVERT: A 209 GLU cc_start: 0.7343 (tt0) cc_final: 0.7071 (tt0) REVERT: A 258 GLU cc_start: 0.7778 (pt0) cc_final: 0.7489 (pt0) REVERT: A 321 ASP cc_start: 0.7469 (t70) cc_final: 0.7076 (t0) REVERT: A 382 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7336 (mt-10) REVERT: B 96 ARG cc_start: 0.7777 (mtt180) cc_final: 0.7541 (mtt180) REVERT: B 124 TYR cc_start: 0.7729 (m-80) cc_final: 0.7314 (m-80) REVERT: B 138 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6323 (mt-10) REVERT: N 5 GLN cc_start: 0.6876 (tp-100) cc_final: 0.6434 (mt0) REVERT: N 82 GLN cc_start: 0.7193 (tp40) cc_final: 0.6925 (tp-100) REVERT: N 94 TYR cc_start: 0.7943 (m-80) cc_final: 0.7627 (m-80) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 1.5250 time to fit residues: 252.4299 Evaluate side-chains 120 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 20 GLN P 24 GLN R 132 ASN R 241 HIS R 336 HIS R 354 HIS A 23 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 269 ASN B 88 ASN B 91 HIS B 176 GLN B 268 ASN B 340 ASN N 31 ASN N 39 GLN N 120 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.165540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.130722 restraints weight = 8683.662| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.64 r_work: 0.3369 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8507 Z= 0.210 Angle : 0.545 8.426 11499 Z= 0.300 Chirality : 0.042 0.146 1277 Planarity : 0.005 0.050 1469 Dihedral : 4.688 24.209 1148 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.12 % Allowed : 12.58 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1030 helix: 0.65 (0.25), residues: 423 sheet: -0.55 (0.33), residues: 218 loop : -1.69 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.017 0.002 PHE R 313 TYR 0.030 0.002 TYR R 146 ARG 0.004 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.987 Fit side-chains REVERT: R 246 ILE cc_start: 0.7802 (mt) cc_final: 0.7564 (mp) REVERT: R 281 GLU cc_start: 0.7393 (tt0) cc_final: 0.7114 (mm-30) REVERT: A 27 GLU cc_start: 0.6875 (tp30) cc_final: 0.6189 (tp30) REVERT: A 58 LYS cc_start: 0.6604 (ttpp) cc_final: 0.5811 (mmmt) REVERT: A 301 TYR cc_start: 0.8227 (m-80) cc_final: 0.7782 (m-80) REVERT: A 346 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6090 (mtp180) REVERT: A 382 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7871 (mt-10) REVERT: B 124 TYR cc_start: 0.7846 (m-80) cc_final: 0.7343 (m-80) REVERT: B 138 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7206 (mt-10) REVERT: B 175 GLN cc_start: 0.7728 (mm110) cc_final: 0.7527 (mm110) REVERT: N 5 GLN cc_start: 0.6994 (tp-100) cc_final: 0.6364 (mt0) REVERT: N 82 GLN cc_start: 0.7367 (tp40) cc_final: 0.7147 (tp-100) REVERT: N 94 TYR cc_start: 0.7980 (m-80) cc_final: 0.7745 (m-80) outliers start: 19 outliers final: 8 residues processed: 143 average time/residue: 1.3285 time to fit residues: 201.5529 Evaluate side-chains 127 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 83 optimal weight: 0.0170 chunk 95 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 176 GLN B 340 ASN N 31 ASN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.166457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.131459 restraints weight = 8940.872| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.68 r_work: 0.3373 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 8507 Z= 0.231 Angle : 0.521 7.521 11499 Z= 0.288 Chirality : 0.041 0.141 1277 Planarity : 0.004 0.047 1469 Dihedral : 4.471 19.109 1148 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.45 % Allowed : 15.92 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1030 helix: 1.33 (0.25), residues: 422 sheet: -0.36 (0.33), residues: 216 loop : -1.55 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.009 0.001 HIS A 220 PHE 0.017 0.001 PHE R 313 TYR 0.024 0.001 TYR R 146 ARG 0.002 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.902 Fit side-chains REVERT: R 165 CYS cc_start: 0.7322 (t) cc_final: 0.6854 (m) REVERT: R 246 ILE cc_start: 0.7748 (mt) cc_final: 0.7489 (mp) REVERT: R 253 LYS cc_start: 0.7742 (tptp) cc_final: 0.7500 (tmtt) REVERT: R 281 GLU cc_start: 0.7341 (tt0) cc_final: 0.7119 (mm-30) REVERT: R 367 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6760 (mp0) REVERT: A 27 GLU cc_start: 0.6852 (tp30) cc_final: 0.6162 (tp30) REVERT: A 58 LYS cc_start: 0.7058 (ttpp) cc_final: 0.6256 (mmmt) REVERT: A 60 MET cc_start: 0.7486 (mmt) cc_final: 0.7053 (mmt) REVERT: A 301 TYR cc_start: 0.8123 (m-80) cc_final: 0.7649 (m-80) REVERT: A 346 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6139 (mtp180) REVERT: A 382 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7432 (mt-10) REVERT: B 124 TYR cc_start: 0.7759 (m-80) cc_final: 0.7222 (m-80) REVERT: B 146 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8264 (tp) REVERT: B 175 GLN cc_start: 0.7711 (mm110) cc_final: 0.7461 (mm110) REVERT: B 325 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8165 (mmt) REVERT: N 5 GLN cc_start: 0.7029 (tp-100) cc_final: 0.6469 (mt0) REVERT: N 94 TYR cc_start: 0.7916 (m-80) cc_final: 0.7695 (m-80) outliers start: 22 outliers final: 8 residues processed: 132 average time/residue: 1.3749 time to fit residues: 192.1314 Evaluate side-chains 131 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 192 ASN A 31 GLN A 254 ASN A 380 GLN B 176 GLN B 340 ASN N 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.167827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132582 restraints weight = 8783.170| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.68 r_work: 0.3391 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8507 Z= 0.175 Angle : 0.497 7.982 11499 Z= 0.272 Chirality : 0.041 0.153 1277 Planarity : 0.004 0.048 1469 Dihedral : 4.327 21.027 1148 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.78 % Allowed : 17.04 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1030 helix: 1.83 (0.25), residues: 421 sheet: -0.23 (0.33), residues: 214 loop : -1.36 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.017 0.001 PHE R 313 TYR 0.023 0.001 TYR R 146 ARG 0.003 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.845 Fit side-chains REVERT: R 133 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6955 (mm-30) REVERT: R 164 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7270 (mt) REVERT: R 165 CYS cc_start: 0.6997 (t) cc_final: 0.6577 (m) REVERT: R 253 LYS cc_start: 0.7825 (tptp) cc_final: 0.7534 (tmtt) REVERT: R 348 ILE cc_start: 0.8162 (mt) cc_final: 0.7923 (mt) REVERT: R 367 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6934 (mp0) REVERT: A 58 LYS cc_start: 0.7104 (ttpp) cc_final: 0.6303 (mmmt) REVERT: A 301 TYR cc_start: 0.8017 (m-80) cc_final: 0.7573 (m-80) REVERT: A 346 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6125 (mtp180) REVERT: A 382 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7353 (mt-10) REVERT: B 124 TYR cc_start: 0.7708 (m-80) cc_final: 0.7197 (m-80) REVERT: B 146 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8271 (tp) REVERT: B 175 GLN cc_start: 0.7668 (mm110) cc_final: 0.7456 (mm110) REVERT: N 5 GLN cc_start: 0.7110 (tp-100) cc_final: 0.6494 (mt0) REVERT: N 94 TYR cc_start: 0.7946 (m-80) cc_final: 0.7710 (m-80) REVERT: N 104 THR cc_start: 0.6861 (p) cc_final: 0.6510 (t) outliers start: 25 outliers final: 7 residues processed: 142 average time/residue: 1.3442 time to fit residues: 201.9637 Evaluate side-chains 131 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 96 optimal weight: 0.0170 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 400 GLN A 31 GLN A 380 GLN B 176 GLN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.170209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.135757 restraints weight = 8680.444| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.62 r_work: 0.3430 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 0.043 8507 Z= 0.178 Angle : 0.487 6.346 11499 Z= 0.267 Chirality : 0.041 0.164 1277 Planarity : 0.004 0.047 1469 Dihedral : 4.255 21.012 1148 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.56 % Allowed : 18.15 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1030 helix: 2.03 (0.25), residues: 421 sheet: -0.17 (0.34), residues: 213 loop : -1.31 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 232 HIS 0.008 0.001 HIS A 220 PHE 0.017 0.001 PHE R 313 TYR 0.022 0.001 TYR R 146 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.045 Fit side-chains REVERT: R 165 CYS cc_start: 0.7093 (t) cc_final: 0.6695 (m) REVERT: R 253 LYS cc_start: 0.7787 (tptp) cc_final: 0.7547 (tmtt) REVERT: R 344 THR cc_start: 0.8137 (m) cc_final: 0.7855 (m) REVERT: R 348 ILE cc_start: 0.8203 (mt) cc_final: 0.7974 (mt) REVERT: R 367 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6871 (mp0) REVERT: A 58 LYS cc_start: 0.7106 (ttpp) cc_final: 0.6319 (mmmt) REVERT: A 301 TYR cc_start: 0.8020 (m-80) cc_final: 0.7637 (m-80) REVERT: A 346 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6238 (mtp180) REVERT: A 382 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7389 (mt-10) REVERT: B 124 TYR cc_start: 0.7730 (m-80) cc_final: 0.7185 (m-80) REVERT: B 146 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8279 (tp) REVERT: B 175 GLN cc_start: 0.7674 (mm110) cc_final: 0.7456 (mm110) REVERT: B 197 ARG cc_start: 0.7190 (mtt-85) cc_final: 0.6774 (mmt90) REVERT: N 5 GLN cc_start: 0.7007 (tp-100) cc_final: 0.6544 (mt0) REVERT: N 94 TYR cc_start: 0.7986 (m-80) cc_final: 0.7714 (m-80) REVERT: N 104 THR cc_start: 0.6950 (p) cc_final: 0.6682 (t) outliers start: 23 outliers final: 7 residues processed: 134 average time/residue: 1.2866 time to fit residues: 183.2213 Evaluate side-chains 126 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 400 GLN A 31 GLN A 380 GLN B 176 GLN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.170218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.135571 restraints weight = 8674.411| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.62 r_work: 0.3416 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8507 Z= 0.179 Angle : 0.483 5.351 11499 Z= 0.265 Chirality : 0.041 0.138 1277 Planarity : 0.004 0.047 1469 Dihedral : 4.218 21.063 1148 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.12 % Allowed : 18.04 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.26), residues: 1030 helix: 2.12 (0.25), residues: 422 sheet: -0.17 (0.33), residues: 216 loop : -1.23 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 232 HIS 0.007 0.001 HIS A 220 PHE 0.016 0.001 PHE R 313 TYR 0.021 0.001 TYR R 146 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.979 Fit side-chains REVERT: R 164 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7222 (mt) REVERT: R 165 CYS cc_start: 0.7135 (t) cc_final: 0.6664 (m) REVERT: R 253 LYS cc_start: 0.7800 (tptp) cc_final: 0.7532 (tmtt) REVERT: R 281 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7241 (mm-30) REVERT: R 344 THR cc_start: 0.8307 (m) cc_final: 0.7997 (m) REVERT: R 348 ILE cc_start: 0.8191 (mt) cc_final: 0.7976 (mt) REVERT: R 367 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6834 (mp0) REVERT: A 58 LYS cc_start: 0.7102 (ttpp) cc_final: 0.6296 (mmmt) REVERT: A 301 TYR cc_start: 0.8020 (m-80) cc_final: 0.7609 (m-80) REVERT: A 346 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6247 (mtp180) REVERT: A 382 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7820 (mt-10) REVERT: B 124 TYR cc_start: 0.7695 (m-80) cc_final: 0.7129 (m-80) REVERT: B 146 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8285 (tp) REVERT: B 197 ARG cc_start: 0.7193 (mtt-85) cc_final: 0.6788 (mmt90) REVERT: N 5 GLN cc_start: 0.6941 (tp-100) cc_final: 0.6510 (mt0) REVERT: N 94 TYR cc_start: 0.7929 (m-80) cc_final: 0.7653 (m-80) REVERT: N 104 THR cc_start: 0.6922 (p) cc_final: 0.6682 (t) outliers start: 28 outliers final: 12 residues processed: 138 average time/residue: 1.2216 time to fit residues: 179.4099 Evaluate side-chains 133 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 192 ASN Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 236 GLU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 400 GLN A 31 GLN A 380 GLN B 176 GLN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.165246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129954 restraints weight = 8777.311| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.66 r_work: 0.3370 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8507 Z= 0.215 Angle : 0.506 5.178 11499 Z= 0.277 Chirality : 0.042 0.153 1277 Planarity : 0.004 0.049 1469 Dihedral : 4.289 21.174 1148 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.12 % Allowed : 18.93 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1030 helix: 2.12 (0.25), residues: 422 sheet: -0.08 (0.34), residues: 219 loop : -1.19 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 232 HIS 0.008 0.001 HIS A 220 PHE 0.018 0.002 PHE R 313 TYR 0.022 0.002 TYR R 146 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.931 Fit side-chains REVERT: R 164 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7336 (mt) REVERT: R 253 LYS cc_start: 0.7837 (tptp) cc_final: 0.7530 (tmtt) REVERT: R 281 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7270 (mm-30) REVERT: R 344 THR cc_start: 0.8135 (m) cc_final: 0.7833 (m) REVERT: R 348 ILE cc_start: 0.8191 (mt) cc_final: 0.7988 (mt) REVERT: R 367 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6854 (mp0) REVERT: A 31 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6749 (tm130) REVERT: A 58 LYS cc_start: 0.7133 (ttpp) cc_final: 0.6275 (mmmt) REVERT: A 223 ASP cc_start: 0.8144 (t0) cc_final: 0.7891 (t70) REVERT: A 301 TYR cc_start: 0.8051 (m-80) cc_final: 0.7647 (m-80) REVERT: A 346 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6207 (mtp180) REVERT: A 382 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7820 (mt-10) REVERT: B 124 TYR cc_start: 0.7700 (m-80) cc_final: 0.7140 (m-80) REVERT: B 146 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8315 (tp) REVERT: N 1 GLN cc_start: 0.6435 (OUTLIER) cc_final: 0.6182 (tt0) REVERT: N 5 GLN cc_start: 0.7011 (tp-100) cc_final: 0.6462 (mt0) REVERT: N 94 TYR cc_start: 0.7949 (m-80) cc_final: 0.7690 (m-80) REVERT: N 104 THR cc_start: 0.7051 (p) cc_final: 0.6784 (t) outliers start: 28 outliers final: 14 residues processed: 139 average time/residue: 1.2472 time to fit residues: 184.4985 Evaluate side-chains 137 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 192 ASN Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 1 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 44 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.0270 chunk 67 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 400 GLN A 380 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.168532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134219 restraints weight = 8787.888| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.58 r_work: 0.3411 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8507 Z= 0.191 Angle : 0.493 5.236 11499 Z= 0.270 Chirality : 0.041 0.151 1277 Planarity : 0.004 0.049 1469 Dihedral : 4.254 21.237 1148 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.78 % Allowed : 19.38 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1030 helix: 2.19 (0.25), residues: 422 sheet: -0.15 (0.34), residues: 221 loop : -1.12 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 232 HIS 0.007 0.001 HIS A 220 PHE 0.017 0.001 PHE R 313 TYR 0.021 0.002 TYR R 146 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.042 Fit side-chains REVERT: R 164 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7373 (mt) REVERT: R 253 LYS cc_start: 0.7767 (tptp) cc_final: 0.7554 (tmtt) REVERT: R 281 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7254 (mm-30) REVERT: R 344 THR cc_start: 0.8178 (m) cc_final: 0.7890 (m) REVERT: R 367 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6891 (mp0) REVERT: A 58 LYS cc_start: 0.7209 (ttpp) cc_final: 0.6406 (mmmt) REVERT: A 223 ASP cc_start: 0.8157 (t0) cc_final: 0.7920 (t70) REVERT: A 301 TYR cc_start: 0.8040 (m-80) cc_final: 0.7650 (m-80) REVERT: A 346 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6262 (mtp180) REVERT: A 382 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7841 (mt-10) REVERT: B 124 TYR cc_start: 0.7796 (m-80) cc_final: 0.7221 (m-80) REVERT: B 146 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8280 (tp) REVERT: N 1 GLN cc_start: 0.6555 (OUTLIER) cc_final: 0.6299 (tt0) REVERT: N 5 GLN cc_start: 0.6988 (tp-100) cc_final: 0.6571 (mt0) REVERT: N 12 VAL cc_start: 0.7549 (p) cc_final: 0.7324 (p) REVERT: N 94 TYR cc_start: 0.7929 (m-80) cc_final: 0.7677 (m-80) REVERT: N 104 THR cc_start: 0.6880 (p) cc_final: 0.6628 (t) outliers start: 25 outliers final: 13 residues processed: 134 average time/residue: 1.2065 time to fit residues: 172.5687 Evaluate side-chains 132 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 192 ASN Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 1 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 20 GLN ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 400 GLN A 31 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.168813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.133933 restraints weight = 8766.364| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.63 r_work: 0.3406 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8507 Z= 0.185 Angle : 0.486 5.083 11499 Z= 0.266 Chirality : 0.041 0.142 1277 Planarity : 0.004 0.049 1469 Dihedral : 4.208 21.085 1148 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.67 % Allowed : 19.82 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.27), residues: 1030 helix: 2.28 (0.25), residues: 419 sheet: 0.01 (0.34), residues: 225 loop : -1.12 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 232 HIS 0.004 0.001 HIS A 220 PHE 0.026 0.001 PHE B 241 TYR 0.021 0.001 TYR R 146 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.924 Fit side-chains REVERT: R 164 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7333 (mt) REVERT: R 253 LYS cc_start: 0.7740 (tptp) cc_final: 0.7475 (tmtt) REVERT: R 367 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6860 (mp0) REVERT: A 58 LYS cc_start: 0.7187 (ttpp) cc_final: 0.6373 (mmmt) REVERT: A 223 ASP cc_start: 0.8056 (t0) cc_final: 0.7794 (t70) REVERT: A 301 TYR cc_start: 0.8025 (m-80) cc_final: 0.7623 (m-80) REVERT: A 346 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6244 (mtp180) REVERT: A 382 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7674 (mt-10) REVERT: B 124 TYR cc_start: 0.7765 (m-80) cc_final: 0.7201 (m-80) REVERT: B 146 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8281 (tp) REVERT: N 1 GLN cc_start: 0.6509 (OUTLIER) cc_final: 0.6250 (tt0) REVERT: N 5 GLN cc_start: 0.7006 (tp-100) cc_final: 0.6518 (mt0) REVERT: N 12 VAL cc_start: 0.7567 (p) cc_final: 0.7348 (p) REVERT: N 94 TYR cc_start: 0.7932 (m-80) cc_final: 0.7681 (m-80) REVERT: N 104 THR cc_start: 0.6879 (p) cc_final: 0.6644 (t) outliers start: 24 outliers final: 13 residues processed: 132 average time/residue: 1.2156 time to fit residues: 170.7024 Evaluate side-chains 131 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 192 ASN Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 1 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 13 optimal weight: 0.0270 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 400 GLN A 380 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.169753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.135080 restraints weight = 8696.232| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.62 r_work: 0.3415 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8507 Z= 0.176 Angle : 0.483 5.051 11499 Z= 0.265 Chirality : 0.041 0.140 1277 Planarity : 0.004 0.049 1469 Dihedral : 4.192 20.880 1148 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.23 % Allowed : 20.49 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.27), residues: 1030 helix: 2.33 (0.25), residues: 419 sheet: -0.02 (0.34), residues: 225 loop : -1.09 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 232 HIS 0.005 0.001 HIS A 220 PHE 0.018 0.002 PHE R 313 TYR 0.021 0.001 TYR R 146 ARG 0.005 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.878 Fit side-chains REVERT: R 164 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7285 (mt) REVERT: R 253 LYS cc_start: 0.7873 (tptp) cc_final: 0.7501 (tmtt) REVERT: R 367 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6825 (mp0) REVERT: A 58 LYS cc_start: 0.7089 (ttpp) cc_final: 0.6294 (mmmt) REVERT: A 301 TYR cc_start: 0.8016 (m-80) cc_final: 0.7590 (m-80) REVERT: A 346 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6259 (mtp180) REVERT: A 382 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7668 (mt-10) REVERT: B 124 TYR cc_start: 0.7731 (m-80) cc_final: 0.7168 (m-80) REVERT: B 146 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8286 (tp) REVERT: N 1 GLN cc_start: 0.6448 (OUTLIER) cc_final: 0.6197 (tt0) REVERT: N 5 GLN cc_start: 0.7036 (tp-100) cc_final: 0.6544 (mt0) REVERT: N 12 VAL cc_start: 0.7503 (p) cc_final: 0.7287 (p) outliers start: 20 outliers final: 12 residues processed: 126 average time/residue: 1.3479 time to fit residues: 180.2589 Evaluate side-chains 123 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 192 ASN Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 1 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 192 ASN R 400 GLN A 31 GLN A 380 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.169383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.134705 restraints weight = 8803.158| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.63 r_work: 0.3412 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8507 Z= 0.180 Angle : 0.489 5.059 11499 Z= 0.268 Chirality : 0.041 0.141 1277 Planarity : 0.004 0.049 1469 Dihedral : 4.185 20.663 1148 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.89 % Allowed : 20.82 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.27), residues: 1030 helix: 2.38 (0.25), residues: 419 sheet: 0.10 (0.33), residues: 224 loop : -1.13 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 232 HIS 0.005 0.001 HIS A 220 PHE 0.017 0.001 PHE R 313 TYR 0.021 0.002 TYR R 146 ARG 0.006 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7165.38 seconds wall clock time: 125 minutes 23.48 seconds (7523.48 seconds total)