Starting phenix.real_space_refine on Mon May 12 01:38:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jkz_36384/05_2025/8jkz_36384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jkz_36384/05_2025/8jkz_36384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jkz_36384/05_2025/8jkz_36384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jkz_36384/05_2025/8jkz_36384.map" model { file = "/net/cci-nas-00/data/ceres_data/8jkz_36384/05_2025/8jkz_36384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jkz_36384/05_2025/8jkz_36384.cif" } resolution = 3.6 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= 0.002 sd= 0.027 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 33 5.16 5 C 5404 2.51 5 N 1443 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8444 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4674 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 23, 'TRANS': 560} Chain: "B" Number of atoms: 3726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3726 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 28, 'TRANS': 440} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.99, per 1000 atoms: 0.59 Number of scatterers: 8444 At special positions: 0 Unit cell: (78.12, 98.28, 122.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 2 15.00 O 1562 8.00 N 1443 7.00 C 5404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 946.4 milliseconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 11 sheets defined 41.5% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 removed outlier: 3.550A pdb=" N GLN A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TYR A 13 " --> pdb=" O PHE A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 33 removed outlier: 3.621A pdb=" N THR A 28 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 29 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 30 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N SER A 31 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 33 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 49 Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.600A pdb=" N SER A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 98 Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 168 through 176 removed outlier: 3.826A pdb=" N SER A 172 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 198 through 217 Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 262 through 276 Processing helix chain 'A' and resid 286 through 297 removed outlier: 4.075A pdb=" N GLN A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.547A pdb=" N ARG A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 406 through 414 removed outlier: 3.965A pdb=" N SER A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 517 through 529 Processing helix chain 'A' and resid 532 through 548 removed outlier: 3.574A pdb=" N GLN A 538 " --> pdb=" O GLN A 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 60 through 71 removed outlier: 3.837A pdb=" N LEU B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.699A pdb=" N ARG B 106 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.948A pdb=" N VAL B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.602A pdb=" N ALA B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 184 through 189 removed outlier: 4.118A pdb=" N LEU B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 209 removed outlier: 3.547A pdb=" N VAL B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 202 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 276 through 295 Processing helix chain 'B' and resid 312 through 321 removed outlier: 3.514A pdb=" N GLN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 430 removed outlier: 4.150A pdb=" N THR B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 458 removed outlier: 3.624A pdb=" N VAL B 447 " --> pdb=" O PRO B 443 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 458 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 184 removed outlier: 6.404A pdb=" N VAL A 138 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N MET A 20 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N PHE A 139 " --> pdb=" O MET A 20 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TRP A 22 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 251 through 252 removed outlier: 6.546A pdb=" N LEU A 251 " --> pdb=" O TYR A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 579 through 580 removed outlier: 3.610A pdb=" N ALA A 330 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 345 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 338 removed outlier: 4.550A pdb=" N LEU A 501 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 380 removed outlier: 3.611A pdb=" N CYS A 345 " --> pdb=" O TYR A 402 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 559 through 561 removed outlier: 3.548A pdb=" N ALA A 569 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.331A pdb=" N ILE B 303 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 332 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE B 305 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ILE B 334 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS B 307 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.331A pdb=" N ILE B 303 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 332 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE B 305 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ILE B 334 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS B 307 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 27 removed outlier: 3.748A pdb=" N ARG B 25 " --> pdb=" O PHE B 21 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.669A pdb=" N VAL B 50 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG B 51 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU B 147 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA B 53 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N TYR B 149 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B 55 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 146 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE B 183 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL B 148 " --> pdb=" O ILE B 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 265 through 267 346 hydrogen bonds defined for protein. 990 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: 2.34 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1378 1.31 - 1.43: 2382 1.43 - 1.56: 4838 1.56 - 1.68: 8 1.68 - 1.81: 51 Bond restraints: 8657 Sorted by residual: bond pdb=" C2D NAD A 601 " pdb=" C3D NAD A 601 " ideal model delta sigma weight residual 1.531 1.243 0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C4B NAD A 601 " pdb=" O4B NAD A 601 " ideal model delta sigma weight residual 1.433 1.681 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C3B NAD A 601 " pdb=" C4B NAD A 601 " ideal model delta sigma weight residual 1.523 1.281 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C4D NAD A 601 " pdb=" O4D NAD A 601 " ideal model delta sigma weight residual 1.445 1.274 0.171 2.00e-02 2.50e+03 7.31e+01 bond pdb=" C7N NAD A 601 " pdb=" N7N NAD A 601 " ideal model delta sigma weight residual 1.328 1.473 -0.145 2.00e-02 2.50e+03 5.25e+01 ... (remaining 8652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 11571 2.64 - 5.28: 154 5.28 - 7.93: 15 7.93 - 10.57: 5 10.57 - 13.21: 3 Bond angle restraints: 11748 Sorted by residual: angle pdb=" C ILE A 390 " pdb=" N PHE A 391 " pdb=" CA PHE A 391 " ideal model delta sigma weight residual 121.54 131.43 -9.89 1.91e+00 2.74e-01 2.68e+01 angle pdb=" O1A NAD A 601 " pdb=" PA NAD A 601 " pdb=" O2A NAD A 601 " ideal model delta sigma weight residual 122.64 109.43 13.21 3.00e+00 1.11e-01 1.94e+01 angle pdb=" C ALA B 9 " pdb=" CA ALA B 9 " pdb=" CB ALA B 9 " ideal model delta sigma weight residual 116.34 110.45 5.89 1.40e+00 5.10e-01 1.77e+01 angle pdb=" O3 NAD A 601 " pdb=" PN NAD A 601 " pdb=" O5D NAD A 601 " ideal model delta sigma weight residual 98.00 109.75 -11.75 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O1N NAD A 601 " pdb=" PN NAD A 601 " pdb=" O2N NAD A 601 " ideal model delta sigma weight residual 120.02 109.43 10.59 3.00e+00 1.11e-01 1.25e+01 ... (remaining 11743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4401 17.98 - 35.96: 593 35.96 - 53.95: 154 53.95 - 71.93: 32 71.93 - 89.91: 15 Dihedral angle restraints: 5195 sinusoidal: 2120 harmonic: 3075 Sorted by residual: dihedral pdb=" CA LEU B 46 " pdb=" C LEU B 46 " pdb=" N PRO B 47 " pdb=" CA PRO B 47 " ideal model delta harmonic sigma weight residual 180.00 152.47 27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA TYR A 374 " pdb=" C TYR A 374 " pdb=" N THR A 375 " pdb=" CA THR A 375 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA MET A 132 " pdb=" C MET A 132 " pdb=" N ASN A 133 " pdb=" CA ASN A 133 " ideal model delta harmonic sigma weight residual -180.00 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 5192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1141 0.070 - 0.140: 130 0.140 - 0.210: 8 0.210 - 0.280: 1 0.280 - 0.351: 1 Chirality restraints: 1281 Sorted by residual: chirality pdb=" C3D NAD A 601 " pdb=" C2D NAD A 601 " pdb=" C4D NAD A 601 " pdb=" O3D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C3B NAD A 601 " pdb=" C2B NAD A 601 " pdb=" C4B NAD A 601 " pdb=" O3B NAD A 601 " both_signs ideal model delta sigma weight residual False -2.71 -2.44 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C2D NAD A 601 " pdb=" C1D NAD A 601 " pdb=" C3D NAD A 601 " pdb=" O2D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.56 -2.37 -0.19 2.00e-01 2.50e+01 9.50e-01 ... (remaining 1278 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 206 " 0.187 9.50e-02 1.11e+02 8.39e-02 4.33e+00 pdb=" NE ARG A 206 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 206 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 206 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 206 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 391 " -0.011 2.00e-02 2.50e+03 1.52e-02 4.06e+00 pdb=" CG PHE A 391 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 391 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 391 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 391 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 391 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 391 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 390 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C ILE A 390 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE A 390 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A 391 " 0.010 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1203 2.76 - 3.29: 8017 3.29 - 3.83: 13547 3.83 - 4.36: 15536 4.36 - 4.90: 27371 Nonbonded interactions: 65674 Sorted by model distance: nonbonded pdb=" OH TYR B 83 " pdb=" O ASN B 436 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR B 277 " pdb=" OD2 ASP B 321 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR A 333 " pdb=" O ALA A 578 " model vdw 2.233 3.040 nonbonded pdb=" OE2 GLU B 330 " pdb=" NH1 ARG B 411 " model vdw 2.267 3.120 nonbonded pdb=" ND2 ASN B 389 " pdb=" OE1 GLN B 392 " model vdw 2.267 3.120 ... (remaining 65669 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 group one per residue 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.220 Find NCS groups from input model: 0.060 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 : 0.007 0.288 8657 Z= 0.383 Angle : 0.735 13.209 11748 Z= 0.398 Chirality : 0.045 0.351 1281 Planarity : 0.004 0.084 1505 Dihedral : 17.975 89.910 3219 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.01 % Favored : 89.90 % Rotamer: Outliers : 1.00 % Allowed : 26.00 % Favored : 73.01 % 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: -1.21 (0.27), residues: 1049 helix: 0.80 (0.27), residues: 388 sheet: -0.76 (0.40), residues: 189 loop : -2.25 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 198 HIS 0.007 0.001 HIS A 52 PHE 0.035 0.002 PHE A 391 TYR 0.013 0.001 TYR B 149 ARG 0.006 0.000 ARG B 69 Details of bonding type rmsd hydrogen bonds : bond 0.18328 ( 323) hydrogen bonds : angle 6.48013 ( 990) covalent geometry : bond 0.00736 ( 8657) covalent geometry : angle 0.73534 (11748) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 92 average time/residue: 0.2596 time to fit residues: 31.6384 Evaluate side-chains 78 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain B residue 257 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS B 317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.156031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.116341 restraints weight = 11852.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.114574 restraints weight = 12893.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.116035 restraints weight = 15359.797| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8657 Z= 0.122 Angle : 0.562 8.625 11748 Z= 0.296 Chirality : 0.041 0.154 1281 Planarity : 0.004 0.038 1505 Dihedral : 7.096 64.174 1212 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.53 % Favored : 90.37 % Rotamer: Outliers : 3.32 % Allowed : 24.45 % Favored : 72.23 % 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: -0.94 (0.27), residues: 1049 helix: 1.15 (0.28), residues: 389 sheet: -0.67 (0.39), residues: 186 loop : -2.20 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 377 HIS 0.007 0.001 HIS A 52 PHE 0.030 0.001 PHE A 391 TYR 0.014 0.001 TYR B 366 ARG 0.004 0.000 ARG A 438 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 323) hydrogen bonds : angle 4.56589 ( 990) covalent geometry : bond 0.00271 ( 8657) covalent geometry : angle 0.56247 (11748) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.7231 (t80) REVERT: A 112 LEU cc_start: 0.4548 (OUTLIER) cc_final: 0.4176 (tt) REVERT: B 98 LEU cc_start: 0.9055 (tt) cc_final: 0.8670 (tt) outliers start: 30 outliers final: 11 residues processed: 109 average time/residue: 0.2115 time to fit residues: 32.2865 Evaluate side-chains 88 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 25 optimal weight: 0.8980 chunk 96 optimal weight: 0.2980 chunk 83 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 8 optimal weight: 0.0060 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS B 45 ASN B 339 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.156970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.118254 restraints weight = 12048.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.116660 restraints weight = 13149.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.118035 restraints weight = 14412.891| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8657 Z= 0.107 Angle : 0.541 8.283 11748 Z= 0.282 Chirality : 0.041 0.155 1281 Planarity : 0.003 0.037 1505 Dihedral : 6.469 61.806 1209 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.34 % Favored : 90.56 % Rotamer: Outliers : 3.32 % Allowed : 24.45 % Favored : 72.23 % 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: -0.71 (0.27), residues: 1049 helix: 1.36 (0.28), residues: 390 sheet: -0.58 (0.40), residues: 185 loop : -2.07 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 377 HIS 0.005 0.001 HIS A 52 PHE 0.012 0.001 PHE A 328 TYR 0.012 0.001 TYR B 366 ARG 0.004 0.000 ARG B 69 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 323) hydrogen bonds : angle 4.22921 ( 990) covalent geometry : bond 0.00234 ( 8657) covalent geometry : angle 0.54086 (11748) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7251 (t80) REVERT: A 112 LEU cc_start: 0.4613 (OUTLIER) cc_final: 0.4275 (tt) REVERT: A 420 PHE cc_start: 0.8460 (t80) cc_final: 0.8001 (t80) REVERT: B 49 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7331 (mm-40) REVERT: B 188 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8647 (mt) REVERT: B 197 MET cc_start: 0.9047 (mmp) cc_final: 0.8768 (mmm) outliers start: 30 outliers final: 15 residues processed: 114 average time/residue: 0.1968 time to fit residues: 31.5472 Evaluate side-chains 95 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 448 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS B 339 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.156163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116930 restraints weight = 11816.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.114190 restraints weight = 14436.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.115899 restraints weight = 13998.145| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8657 Z= 0.110 Angle : 0.537 8.369 11748 Z= 0.279 Chirality : 0.041 0.169 1281 Planarity : 0.003 0.036 1505 Dihedral : 6.157 56.897 1209 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.15 % Favored : 90.75 % Rotamer: Outliers : 3.43 % Allowed : 25.00 % Favored : 71.57 % 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: -0.61 (0.27), residues: 1049 helix: 1.49 (0.28), residues: 390 sheet: -0.53 (0.40), residues: 185 loop : -2.06 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 377 HIS 0.005 0.001 HIS A 52 PHE 0.054 0.001 PHE A 391 TYR 0.012 0.001 TYR B 366 ARG 0.005 0.000 ARG B 69 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 323) hydrogen bonds : angle 4.07916 ( 990) covalent geometry : bond 0.00248 ( 8657) covalent geometry : angle 0.53685 (11748) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7306 (t80) REVERT: A 112 LEU cc_start: 0.4562 (OUTLIER) cc_final: 0.4261 (tt) REVERT: B 49 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7500 (mm-40) REVERT: B 197 MET cc_start: 0.9038 (mmp) cc_final: 0.8784 (mmm) outliers start: 31 outliers final: 19 residues processed: 105 average time/residue: 0.2084 time to fit residues: 30.6068 Evaluate side-chains 99 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 67 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS B 339 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.152456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113919 restraints weight = 11849.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.111108 restraints weight = 13125.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.112801 restraints weight = 13768.722| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8657 Z= 0.177 Angle : 0.585 8.306 11748 Z= 0.308 Chirality : 0.043 0.159 1281 Planarity : 0.004 0.036 1505 Dihedral : 6.373 52.738 1209 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.20 % Favored : 89.70 % Rotamer: Outliers : 4.31 % Allowed : 24.45 % Favored : 71.24 % 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: -0.77 (0.27), residues: 1049 helix: 1.43 (0.28), residues: 388 sheet: -0.68 (0.39), residues: 187 loop : -2.18 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 377 HIS 0.007 0.001 HIS A 52 PHE 0.019 0.002 PHE A 9 TYR 0.014 0.001 TYR B 366 ARG 0.005 0.000 ARG B 69 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 323) hydrogen bonds : angle 4.19793 ( 990) covalent geometry : bond 0.00424 ( 8657) covalent geometry : angle 0.58537 (11748) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 80 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: A 93 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7373 (t80) REVERT: A 112 LEU cc_start: 0.4616 (OUTLIER) cc_final: 0.4264 (tt) REVERT: A 372 LEU cc_start: 0.8728 (mt) cc_final: 0.8313 (mp) REVERT: B 49 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7549 (mm-40) outliers start: 39 outliers final: 24 residues processed: 111 average time/residue: 0.2053 time to fit residues: 31.6921 Evaluate side-chains 101 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 15 optimal weight: 0.0870 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.155927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.116966 restraints weight = 11798.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.114489 restraints weight = 13542.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.116410 restraints weight = 14985.564| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8657 Z= 0.105 Angle : 0.536 7.939 11748 Z= 0.278 Chirality : 0.040 0.185 1281 Planarity : 0.003 0.035 1505 Dihedral : 6.105 50.780 1209 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.77 % Favored : 91.13 % Rotamer: Outliers : 3.87 % Allowed : 25.33 % Favored : 70.80 % 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: -0.58 (0.27), residues: 1049 helix: 1.53 (0.28), residues: 389 sheet: -0.47 (0.40), residues: 185 loop : -2.07 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 377 HIS 0.005 0.001 HIS A 46 PHE 0.058 0.001 PHE A 391 TYR 0.011 0.001 TYR B 366 ARG 0.005 0.000 ARG B 69 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 323) hydrogen bonds : angle 4.06242 ( 990) covalent geometry : bond 0.00232 ( 8657) covalent geometry : angle 0.53553 (11748) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7360 (t80) REVERT: A 112 LEU cc_start: 0.4646 (OUTLIER) cc_final: 0.4355 (tt) REVERT: A 372 LEU cc_start: 0.8777 (mt) cc_final: 0.8345 (mp) outliers start: 35 outliers final: 24 residues processed: 107 average time/residue: 0.2039 time to fit residues: 30.7261 Evaluate side-chains 96 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 448 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 40 optimal weight: 10.0000 chunk 82 optimal weight: 0.1980 chunk 5 optimal weight: 0.0980 chunk 49 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS B 238 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.152772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.113405 restraints weight = 11985.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.111031 restraints weight = 13751.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111882 restraints weight = 16340.480| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8657 Z= 0.113 Angle : 0.546 8.268 11748 Z= 0.283 Chirality : 0.041 0.169 1281 Planarity : 0.003 0.034 1505 Dihedral : 6.020 51.884 1209 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.44 % Favored : 90.47 % Rotamer: Outliers : 3.87 % Allowed : 25.44 % Favored : 70.69 % 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: -0.56 (0.27), residues: 1049 helix: 1.52 (0.28), residues: 389 sheet: -0.41 (0.40), residues: 185 loop : -2.05 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 377 HIS 0.005 0.001 HIS A 52 PHE 0.010 0.001 PHE B 137 TYR 0.012 0.001 TYR A 402 ARG 0.005 0.000 ARG B 69 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 323) hydrogen bonds : angle 4.07322 ( 990) covalent geometry : bond 0.00259 ( 8657) covalent geometry : angle 0.54572 (11748) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7332 (t80) REVERT: A 112 LEU cc_start: 0.4503 (OUTLIER) cc_final: 0.4198 (tt) REVERT: A 372 LEU cc_start: 0.8780 (mt) cc_final: 0.8350 (mp) REVERT: B 146 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8696 (tt) REVERT: B 373 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7770 (mp0) outliers start: 35 outliers final: 22 residues processed: 105 average time/residue: 0.1910 time to fit residues: 28.5463 Evaluate side-chains 97 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 448 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 65 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 49 optimal weight: 0.0040 chunk 99 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.151852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.112935 restraints weight = 12037.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109899 restraints weight = 14795.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.111747 restraints weight = 15397.056| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8657 Z= 0.134 Angle : 0.555 8.024 11748 Z= 0.289 Chirality : 0.041 0.180 1281 Planarity : 0.004 0.035 1505 Dihedral : 6.095 52.485 1209 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.34 % Favored : 90.56 % Rotamer: Outliers : 3.43 % Allowed : 25.66 % Favored : 70.91 % 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: -0.63 (0.27), residues: 1049 helix: 1.49 (0.28), residues: 388 sheet: -0.51 (0.40), residues: 187 loop : -2.10 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 377 HIS 0.005 0.001 HIS A 52 PHE 0.063 0.002 PHE A 391 TYR 0.012 0.001 TYR B 366 ARG 0.006 0.000 ARG B 69 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 323) hydrogen bonds : angle 4.09569 ( 990) covalent geometry : bond 0.00318 ( 8657) covalent geometry : angle 0.55501 (11748) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7797 (mp10) REVERT: A 93 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7427 (t80) REVERT: A 112 LEU cc_start: 0.4546 (OUTLIER) cc_final: 0.4216 (tt) REVERT: A 372 LEU cc_start: 0.8769 (mt) cc_final: 0.8349 (mp) REVERT: B 373 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7745 (mp0) outliers start: 31 outliers final: 21 residues processed: 100 average time/residue: 0.1849 time to fit residues: 26.4150 Evaluate side-chains 97 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 448 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 chunk 65 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 98 optimal weight: 0.0070 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.153118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.114638 restraints weight = 12001.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111554 restraints weight = 13962.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.112868 restraints weight = 15374.581| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8657 Z= 0.114 Angle : 0.556 9.209 11748 Z= 0.287 Chirality : 0.041 0.222 1281 Planarity : 0.003 0.034 1505 Dihedral : 6.001 54.212 1209 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.25 % Favored : 90.66 % Rotamer: Outliers : 3.21 % Allowed : 25.55 % Favored : 71.24 % 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: -0.57 (0.27), residues: 1049 helix: 1.49 (0.28), residues: 389 sheet: -0.42 (0.40), residues: 185 loop : -2.04 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 377 HIS 0.005 0.001 HIS A 52 PHE 0.010 0.001 PHE B 471 TYR 0.011 0.001 TYR B 366 ARG 0.005 0.000 ARG B 69 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 323) hydrogen bonds : angle 4.05118 ( 990) covalent geometry : bond 0.00261 ( 8657) covalent geometry : angle 0.55603 (11748) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7436 (t80) REVERT: A 112 LEU cc_start: 0.4560 (OUTLIER) cc_final: 0.4247 (tt) REVERT: A 372 LEU cc_start: 0.8766 (mt) cc_final: 0.8339 (mp) REVERT: B 373 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7778 (mp0) outliers start: 29 outliers final: 21 residues processed: 106 average time/residue: 0.1862 time to fit residues: 28.2746 Evaluate side-chains 96 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 98 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.0070 chunk 46 optimal weight: 2.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.150688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111224 restraints weight = 11987.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.108461 restraints weight = 12671.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109430 restraints weight = 16148.634| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8657 Z= 0.134 Angle : 0.561 7.920 11748 Z= 0.291 Chirality : 0.041 0.153 1281 Planarity : 0.003 0.035 1505 Dihedral : 6.083 54.784 1209 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 2.99 % Allowed : 25.44 % Favored : 71.57 % 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: -0.61 (0.27), residues: 1049 helix: 1.50 (0.28), residues: 388 sheet: -0.48 (0.40), residues: 187 loop : -2.09 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 377 HIS 0.006 0.001 HIS A 52 PHE 0.040 0.001 PHE A 391 TYR 0.021 0.001 TYR A 402 ARG 0.006 0.000 ARG B 69 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 323) hydrogen bonds : angle 4.08825 ( 990) covalent geometry : bond 0.00318 ( 8657) covalent geometry : angle 0.56148 (11748) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7787 (mp10) REVERT: A 93 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7479 (t80) REVERT: A 112 LEU cc_start: 0.4206 (OUTLIER) cc_final: 0.3894 (tt) REVERT: A 372 LEU cc_start: 0.8785 (mt) cc_final: 0.8361 (mp) REVERT: B 373 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7741 (mp0) outliers start: 27 outliers final: 21 residues processed: 98 average time/residue: 0.2154 time to fit residues: 29.6763 Evaluate side-chains 95 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 15 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110345 restraints weight = 12140.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.107616 restraints weight = 14325.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.108763 restraints weight = 16660.616| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8657 Z= 0.191 Angle : 0.611 7.863 11748 Z= 0.319 Chirality : 0.043 0.195 1281 Planarity : 0.004 0.036 1505 Dihedral : 6.380 55.680 1209 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 3.10 % Allowed : 25.33 % Favored : 71.57 % 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: -0.77 (0.27), residues: 1049 helix: 1.36 (0.28), residues: 390 sheet: -0.59 (0.40), residues: 187 loop : -2.18 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 377 HIS 0.007 0.001 HIS A 52 PHE 0.018 0.002 PHE A 9 TYR 0.016 0.001 TYR A 402 ARG 0.006 0.000 ARG B 69 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 323) hydrogen bonds : angle 4.21184 ( 990) covalent geometry : bond 0.00463 ( 8657) covalent geometry : angle 0.61083 (11748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2485.18 seconds wall clock time: 44 minutes 21.05 seconds (2661.05 seconds total)