Starting phenix.real_space_refine on Fri Jul 3 00:39:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsb_61769/07_2026/9jsb_61769.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsb_61769/07_2026/9jsb_61769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jsb_61769/07_2026/9jsb_61769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsb_61769/07_2026/9jsb_61769.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jsb_61769/07_2026/9jsb_61769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsb_61769/07_2026/9jsb_61769.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.102 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 40 5.16 5 C 7222 2.51 5 N 1996 2.21 5 O 2166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11436 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3819 Classifications: {'peptide': 483} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 456} Chain: "D" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1793 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain breaks: 3 Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'RNA': 5} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'RNA': 5} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "B" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3819 Classifications: {'peptide': 483} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 456} Chain: "E" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1793 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.32, per 1000 atoms: 0.20 Number of scatterers: 11436 At special positions: 0 Unit cell: (118.15, 97.75, 93.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 10 15.00 Mg 2 11.99 O 2166 8.00 N 1996 7.00 C 7222 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: 0.89 Conformation dependent library (CDL) restraints added in 504.8 milliseconds 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 22 sheets defined 30.0% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 removed outlier: 3.736A pdb=" N GLU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 63 Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 117 through 138 removed outlier: 3.746A pdb=" N VAL A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 164 removed outlier: 3.943A pdb=" N LYS A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.591A pdb=" N THR A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 241 removed outlier: 3.957A pdb=" N THR A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 327 Processing helix chain 'A' and resid 343 through 355 Processing helix chain 'A' and resid 429 through 438 Processing helix chain 'A' and resid 455 through 468 removed outlier: 3.943A pdb=" N ALA A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 484 removed outlier: 3.558A pdb=" N LYS A 483 " --> pdb=" O ASP A 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 225 removed outlier: 3.610A pdb=" N GLU D 224 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE D 225 " --> pdb=" O CYS D 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 221 through 225' Processing helix chain 'D' and resid 235 through 240 removed outlier: 4.047A pdb=" N LEU D 239 " --> pdb=" O ASN D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 261 removed outlier: 3.669A pdb=" N GLN D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'B' and resid 23 through 31 removed outlier: 3.599A pdb=" N ALA B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 64 Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 117 through 137 removed outlier: 3.796A pdb=" N VAL B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 164 removed outlier: 3.538A pdb=" N ARG B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 190 Processing helix chain 'B' and resid 201 through 206 removed outlier: 3.597A pdb=" N ILE B 205 " --> pdb=" O TRP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 225 through 230 removed outlier: 3.512A pdb=" N THR B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 240 removed outlier: 3.901A pdb=" N THR B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 327 Processing helix chain 'B' and resid 343 through 355 Processing helix chain 'B' and resid 429 through 439 Processing helix chain 'B' and resid 455 through 468 removed outlier: 4.017A pdb=" N ALA B 461 " --> pdb=" O PRO B 457 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 484 removed outlier: 3.613A pdb=" N LYS B 483 " --> pdb=" O ASP B 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 231 removed outlier: 3.696A pdb=" N GLN E 230 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL E 231 " --> pdb=" O ILE E 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 227 through 231' Processing helix chain 'E' and resid 235 through 240 removed outlier: 4.325A pdb=" N LEU E 239 " --> pdb=" O ASN E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 261 removed outlier: 3.568A pdb=" N TYR E 261 " --> pdb=" O GLN E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 377 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 43 removed outlier: 3.569A pdb=" N ILE A 42 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 95 " --> pdb=" O ILE A 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48 removed outlier: 3.534A pdb=" N GLY A 48 " --> pdb=" O ALA A 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 150 removed outlier: 3.696A pdb=" N LEU A 150 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AA6, first strand: chain 'A' and resid 297 through 300 removed outlier: 7.514A pdb=" N HIS A 304 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 334 through 338 removed outlier: 6.694A pdb=" N VAL A 334 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL A 365 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE A 336 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AA9, first strand: chain 'D' and resid 324 through 328 removed outlier: 4.642A pdb=" N TRP D 334 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 336 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET D 402 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 179 through 181 Processing sheet with id=AB2, first strand: chain 'D' and resid 267 through 270 removed outlier: 3.639A pdb=" N ALA D 275 " --> pdb=" O ASP D 270 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 288 through 291 removed outlier: 3.895A pdb=" N TYR D 291 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR D 298 " --> pdb=" O TYR D 291 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.621A pdb=" N ARG B 6 " --> pdb=" O PHE B 388 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 388 " --> pdb=" O ARG B 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 13 through 15 Processing sheet with id=AB6, first strand: chain 'B' and resid 41 through 43 removed outlier: 5.928A pdb=" N ILE B 42 " --> pdb=" O GLU B 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AB8, first strand: chain 'B' and resid 288 through 289 removed outlier: 3.612A pdb=" N PHE B 282 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N CYS B 259 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU B 337 " --> pdb=" O CYS B 259 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL B 261 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL B 334 " --> pdb=" O ASP B 363 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL B 365 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 336 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL B 367 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LYS B 338 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLU B 369 " --> pdb=" O LYS B 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 297 through 300 removed outlier: 7.500A pdb=" N HIS B 304 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 168 through 169 Processing sheet with id=AC2, first strand: chain 'E' and resid 171 through 172 removed outlier: 3.762A pdb=" N MET E 402 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 267 through 270 removed outlier: 3.640A pdb=" N ALA E 275 " --> pdb=" O ASP E 270 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 289 through 291 305 hydrogen bonds defined for protein. 867 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: 1.69 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3469 1.34 - 1.46: 2300 1.46 - 1.58: 5867 1.58 - 1.70: 18 1.70 - 1.82: 72 Bond restraints: 11726 Sorted by residual: bond pdb=" CA ARG D 372 " pdb=" C ARG D 372 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.30e-02 5.92e+03 4.78e+00 bond pdb=" C CYS A 421 " pdb=" O CYS A 421 " ideal model delta sigma weight residual 1.246 1.230 0.016 9.20e-03 1.18e+04 2.90e+00 bond pdb=" CA ILE A 375 " pdb=" C ILE A 375 " ideal model delta sigma weight residual 1.526 1.507 0.019 1.16e-02 7.43e+03 2.61e+00 bond pdb=" CA HIS E 273 " pdb=" CB HIS E 273 " ideal model delta sigma weight residual 1.530 1.556 -0.026 1.69e-02 3.50e+03 2.29e+00 bond pdb=" C PRO A 79 " pdb=" O PRO A 79 " ideal model delta sigma weight residual 1.243 1.231 0.012 8.50e-03 1.38e+04 2.00e+00 ... (remaining 11721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 15425 2.03 - 4.06: 387 4.06 - 6.09: 76 6.09 - 8.12: 13 8.12 - 10.15: 5 Bond angle restraints: 15906 Sorted by residual: angle pdb=" N GLY D 373 " pdb=" CA GLY D 373 " pdb=" C GLY D 373 " ideal model delta sigma weight residual 112.50 108.06 4.44 1.16e+00 7.43e-01 1.47e+01 angle pdb=" C CYS D 222 " pdb=" N SER D 223 " pdb=" CA SER D 223 " ideal model delta sigma weight residual 121.54 128.76 -7.22 1.91e+00 2.74e-01 1.43e+01 angle pdb=" N ILE B 456 " pdb=" CA ILE B 456 " pdb=" C ILE B 456 " ideal model delta sigma weight residual 108.88 117.05 -8.17 2.16e+00 2.14e-01 1.43e+01 angle pdb=" N GLY A 379 " pdb=" CA GLY A 379 " pdb=" C GLY A 379 " ideal model delta sigma weight residual 111.66 118.65 -6.99 1.91e+00 2.74e-01 1.34e+01 angle pdb=" CA TYR A 381 " pdb=" C TYR A 381 " pdb=" N PRO A 382 " ideal model delta sigma weight residual 120.79 117.31 3.48 9.70e-01 1.06e+00 1.29e+01 ... (remaining 15901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.12: 6437 30.12 - 60.23: 551 60.23 - 90.35: 39 90.35 - 120.46: 0 120.46 - 150.58: 1 Dihedral angle restraints: 7028 sinusoidal: 2976 harmonic: 4052 Sorted by residual: dihedral pdb=" O4' U H 2 " pdb=" C1' U H 2 " pdb=" N1 U H 2 " pdb=" C2 U H 2 " ideal model delta sinusoidal sigma weight residual 200.00 49.42 150.58 1 1.50e+01 4.44e-03 7.98e+01 dihedral pdb=" CA GLN B 452 " pdb=" C GLN B 452 " pdb=" N ARG B 453 " pdb=" CA ARG B 453 " ideal model delta harmonic sigma weight residual 180.00 152.23 27.77 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA TYR B 381 " pdb=" C TYR B 381 " pdb=" N PRO B 382 " pdb=" CA PRO B 382 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 7025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1256 0.049 - 0.098: 359 0.098 - 0.147: 76 0.147 - 0.196: 14 0.196 - 0.245: 5 Chirality restraints: 1710 Sorted by residual: chirality pdb=" CB THR B 441 " pdb=" CA THR B 441 " pdb=" OG1 THR B 441 " pdb=" CG2 THR B 441 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB THR D 183 " pdb=" CA THR D 183 " pdb=" OG1 THR D 183 " pdb=" CG2 THR D 183 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE B 263 " pdb=" CA ILE B 263 " pdb=" CG1 ILE B 263 " pdb=" CG2 ILE B 263 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1707 not shown) Planarity restraints: 2032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 198 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO D 199 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO D 199 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO D 199 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 273 " 0.016 2.00e-02 2.50e+03 2.14e-02 6.88e+00 pdb=" CG HIS E 273 " -0.045 2.00e-02 2.50e+03 pdb=" ND1 HIS E 273 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS E 273 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 HIS E 273 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS E 273 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS E 273 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C HIS E 273 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS E 273 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS E 274 " -0.014 2.00e-02 2.50e+03 ... (remaining 2029 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 176 2.65 - 3.21: 9696 3.21 - 3.78: 18165 3.78 - 4.34: 23963 4.34 - 4.90: 39259 Nonbonded interactions: 91259 Sorted by model distance: nonbonded pdb=" OD1 ASN A 446 " pdb="MG MG A 501 " model vdw 2.088 2.170 nonbonded pdb=" OD1 ASN B 446 " pdb="MG MG B 501 " model vdw 2.094 2.170 nonbonded pdb=" O PHE B 438 " pdb=" OG1 THR B 441 " model vdw 2.249 3.040 nonbonded pdb=" OP1 A H 3 " pdb="MG MG B 501 " model vdw 2.249 2.170 nonbonded pdb=" OE1 GLN A 273 " pdb=" OG1 THR B 298 " model vdw 2.255 3.040 ... (remaining 91254 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.410 Find NCS groups from input model: 0.170 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:9.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 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 0.061 11726 Z= 0.190 Angle : 0.781 10.155 15906 Z= 0.432 Chirality : 0.048 0.245 1710 Planarity : 0.006 0.109 2032 Dihedral : 19.705 150.577 4428 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 1.59 % Allowed : 35.54 % Favored : 62.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.20), residues: 1384 helix: -1.18 (0.24), residues: 360 sheet: -2.01 (0.38), residues: 202 loop : -3.06 (0.18), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 249 TYR 0.021 0.002 TYR A 398 PHE 0.031 0.002 PHE E 202 TRP 0.020 0.002 TRP E 212 HIS 0.027 0.001 HIS E 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (11726) covalent geometry : angle 0.78117 / 0.43 (15906) hydrogen bonds : bond 0.18045 / 12.03 ( 305) hydrogen bonds : angle 8.02866 / 5.93 ( 867) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.505 Fit side-chains REVERT: A 237 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6454 (tp) outliers start: 19 outliers final: 4 residues processed: 138 average time/residue: 0.5383 time to fit residues: 81.1976 Evaluate side-chains 115 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain E residue 205 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 HIS ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 ASN ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 HIS ** E 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.231598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.203925 restraints weight = 13821.119| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 2.03 r_work: 0.4168 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.115 11726 Z= 0.429 Angle : 0.990 17.313 15906 Z= 0.514 Chirality : 0.058 0.335 1710 Planarity : 0.008 0.078 2032 Dihedral : 10.474 165.550 1692 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.86 % Favored : 86.99 % Rotamer: Outliers : 9.45 % Allowed : 31.69 % Favored : 58.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.19), residues: 1384 helix: -1.06 (0.25), residues: 380 sheet: -2.76 (0.35), residues: 216 loop : -3.39 (0.17), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 287 TYR 0.033 0.004 TYR A 398 PHE 0.042 0.004 PHE B 335 TRP 0.022 0.004 TRP E 212 HIS 0.010 0.002 HIS E 273 Details of bonding type rmsd/Z covalent geometry : bond 0.01003 / 0.43 (11726) covalent geometry : angle 0.98968 / 0.51 (15906) hydrogen bonds : bond 0.07238 / 4.70 ( 305) hydrogen bonds : angle 6.85660 / 4.92 ( 867) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 130 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 6 ARG cc_start: 0.5974 (OUTLIER) cc_final: 0.4530 (ttp-170) REVERT: A 14 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.4815 (tm-30) REVERT: A 255 GLU cc_start: 0.6897 (mp0) cc_final: 0.6260 (mp0) REVERT: A 303 ARG cc_start: 0.7677 (mtp85) cc_final: 0.7343 (mtt180) REVERT: A 468 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7637 (mp) REVERT: D 237 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7390 (ttmm) REVERT: D 281 ILE cc_start: 0.1940 (OUTLIER) cc_final: 0.0374 (tt) REVERT: B 8 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.4676 (m-80) REVERT: B 208 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.6699 (ttpt) REVERT: B 248 ARG cc_start: 0.5699 (OUTLIER) cc_final: 0.5345 (ptt180) REVERT: E 256 ARG cc_start: 0.5674 (OUTLIER) cc_final: 0.5404 (ttp80) REVERT: E 349 TYR cc_start: 0.4795 (p90) cc_final: 0.3955 (p90) outliers start: 113 outliers final: 54 residues processed: 220 average time/residue: 0.5396 time to fit residues: 129.4312 Evaluate side-chains 188 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 125 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 248 ARG Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 402 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 5 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 ASN B 224 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN E 273 HIS E 352 HIS E 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.238758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.210686 restraints weight = 13971.705| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 2.07 r_work: 0.4250 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11726 Z= 0.144 Angle : 0.650 8.219 15906 Z= 0.342 Chirality : 0.043 0.181 1710 Planarity : 0.005 0.060 2032 Dihedral : 9.838 160.663 1691 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 6.10 % Allowed : 34.62 % Favored : 59.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.20), residues: 1384 helix: -0.44 (0.26), residues: 380 sheet: -1.85 (0.41), residues: 168 loop : -3.36 (0.17), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 380 TYR 0.026 0.002 TYR A 398 PHE 0.014 0.002 PHE D 289 TRP 0.018 0.002 TRP D 378 HIS 0.009 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (11726) covalent geometry : angle 0.65038 / 0.34 (15906) hydrogen bonds : bond 0.04552 / 3.05 ( 305) hydrogen bonds : angle 5.96672 / 4.41 ( 867) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 126 time to evaluate : 0.445 Fit side-chains REVERT: A 6 ARG cc_start: 0.5688 (OUTLIER) cc_final: 0.4333 (ttp-170) REVERT: A 255 GLU cc_start: 0.6863 (mp0) cc_final: 0.6269 (mp0) REVERT: A 297 ARG cc_start: 0.6461 (ttm170) cc_final: 0.6127 (mtt-85) REVERT: A 303 ARG cc_start: 0.7570 (mtp85) cc_final: 0.7218 (mtt180) REVERT: D 237 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7160 (ttmm) REVERT: B 8 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.4461 (m-80) REVERT: B 248 ARG cc_start: 0.5311 (OUTLIER) cc_final: 0.4961 (ptt180) REVERT: B 380 ASN cc_start: 0.5280 (OUTLIER) cc_final: 0.4971 (p0) REVERT: B 436 GLU cc_start: 0.5542 (OUTLIER) cc_final: 0.5258 (tp30) REVERT: B 468 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7463 (mp) REVERT: E 254 LEU cc_start: 0.5864 (OUTLIER) cc_final: 0.4678 (tt) REVERT: E 326 ARG cc_start: 0.4616 (OUTLIER) cc_final: 0.3686 (ttm110) REVERT: E 330 MET cc_start: 0.6306 (mpt) cc_final: 0.5950 (mpt) outliers start: 73 outliers final: 30 residues processed: 187 average time/residue: 0.4981 time to fit residues: 102.0047 Evaluate side-chains 155 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 248 ARG Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 341 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 50 optimal weight: 0.0570 chunk 99 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 HIS ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN E 273 HIS E 352 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.241653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.214377 restraints weight = 13966.715| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 2.06 r_work: 0.4289 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11726 Z= 0.116 Angle : 0.587 8.167 15906 Z= 0.307 Chirality : 0.042 0.151 1710 Planarity : 0.004 0.051 2032 Dihedral : 9.420 157.999 1688 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 6.02 % Allowed : 34.62 % Favored : 59.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.20), residues: 1384 helix: -0.17 (0.27), residues: 380 sheet: -2.66 (0.39), residues: 162 loop : -3.13 (0.17), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 380 TYR 0.021 0.001 TYR B 398 PHE 0.012 0.001 PHE A 275 TRP 0.015 0.001 TRP E 212 HIS 0.005 0.001 HIS E 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (11726) covalent geometry : angle 0.58715 / 0.31 (15906) hydrogen bonds : bond 0.03720 / 2.52 ( 305) hydrogen bonds : angle 5.58383 / 4.19 ( 867) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 121 time to evaluate : 0.471 Fit side-chains REVERT: A 6 ARG cc_start: 0.5619 (OUTLIER) cc_final: 0.4302 (ttp-170) REVERT: A 255 GLU cc_start: 0.6835 (mp0) cc_final: 0.6262 (mp0) REVERT: A 303 ARG cc_start: 0.7445 (mtp85) cc_final: 0.7052 (mtt180) REVERT: D 237 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7126 (ttmm) REVERT: B 8 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.4417 (m-80) REVERT: B 14 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.4557 (tm-30) REVERT: B 248 ARG cc_start: 0.5269 (OUTLIER) cc_final: 0.3632 (ppp-140) REVERT: B 380 ASN cc_start: 0.5169 (OUTLIER) cc_final: 0.4921 (p0) REVERT: B 468 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7392 (mp) REVERT: E 254 LEU cc_start: 0.5846 (OUTLIER) cc_final: 0.4679 (tt) REVERT: E 326 ARG cc_start: 0.4480 (OUTLIER) cc_final: 0.3550 (ttm110) REVERT: E 330 MET cc_start: 0.6162 (mpt) cc_final: 0.5827 (mpt) outliers start: 72 outliers final: 30 residues processed: 183 average time/residue: 0.4497 time to fit residues: 90.5803 Evaluate side-chains 151 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 248 ARG Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 376 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 0.0470 overall best weight: 1.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 273 HIS E 352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.239363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.211813 restraints weight = 13992.810| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 2.05 r_work: 0.4262 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11726 Z= 0.154 Angle : 0.622 9.008 15906 Z= 0.323 Chirality : 0.043 0.159 1710 Planarity : 0.005 0.046 2032 Dihedral : 9.458 159.673 1688 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 6.77 % Allowed : 34.53 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.20), residues: 1384 helix: -0.10 (0.27), residues: 380 sheet: -2.73 (0.38), residues: 162 loop : -3.10 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 377 TYR 0.020 0.002 TYR B 398 PHE 0.017 0.002 PHE B 335 TRP 0.014 0.002 TRP E 212 HIS 0.006 0.001 HIS E 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (11726) covalent geometry : angle 0.62211 / 0.32 (15906) hydrogen bonds : bond 0.03929 / 2.63 ( 305) hydrogen bonds : angle 5.58754 / 4.17 ( 867) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 114 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 6 ARG cc_start: 0.5663 (OUTLIER) cc_final: 0.4321 (ttp-170) REVERT: A 255 GLU cc_start: 0.6875 (mp0) cc_final: 0.6148 (mp0) REVERT: A 297 ARG cc_start: 0.6489 (ttm170) cc_final: 0.6151 (mtt-85) REVERT: A 303 ARG cc_start: 0.7481 (mtp85) cc_final: 0.7114 (mtt180) REVERT: D 237 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7229 (ttmm) REVERT: B 8 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.4397 (m-80) REVERT: B 14 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.4816 (tm-30) REVERT: B 380 ASN cc_start: 0.5170 (OUTLIER) cc_final: 0.4913 (p0) REVERT: B 403 MET cc_start: 0.6530 (OUTLIER) cc_final: 0.5937 (mmm) REVERT: B 436 GLU cc_start: 0.5298 (OUTLIER) cc_final: 0.4182 (tp30) REVERT: B 468 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7471 (mp) REVERT: E 254 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.4695 (tt) REVERT: E 281 ILE cc_start: 0.1994 (OUTLIER) cc_final: 0.0424 (tt) REVERT: E 326 ARG cc_start: 0.4474 (OUTLIER) cc_final: 0.3532 (ttm110) outliers start: 81 outliers final: 44 residues processed: 181 average time/residue: 0.4616 time to fit residues: 91.7785 Evaluate side-chains 164 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 109 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 376 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 132 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 HIS E 352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.236228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.207703 restraints weight = 13948.614| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 2.05 r_work: 0.4227 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11726 Z= 0.203 Angle : 0.684 11.461 15906 Z= 0.355 Chirality : 0.046 0.197 1710 Planarity : 0.005 0.045 2032 Dihedral : 9.631 161.216 1688 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 8.11 % Allowed : 33.61 % Favored : 58.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.21), residues: 1384 helix: -0.18 (0.27), residues: 382 sheet: -2.54 (0.39), residues: 182 loop : -3.22 (0.18), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 377 TYR 0.024 0.002 TYR B 398 PHE 0.022 0.002 PHE B 335 TRP 0.018 0.002 TRP E 212 HIS 0.007 0.001 HIS E 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (11726) covalent geometry : angle 0.68379 / 0.35 (15906) hydrogen bonds : bond 0.04454 / 2.98 ( 305) hydrogen bonds : angle 5.78274 / 4.29 ( 867) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 119 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 6 ARG cc_start: 0.5819 (OUTLIER) cc_final: 0.4383 (ttp-170) REVERT: A 14 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.4918 (tm-30) REVERT: A 237 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6118 (tp) REVERT: A 255 GLU cc_start: 0.6917 (mp0) cc_final: 0.6198 (mp0) REVERT: A 297 ARG cc_start: 0.6575 (ttm170) cc_final: 0.6199 (mtt-85) REVERT: A 303 ARG cc_start: 0.7560 (mtp85) cc_final: 0.7207 (mtt180) REVERT: D 281 ILE cc_start: 0.2027 (OUTLIER) cc_final: 0.0262 (tt) REVERT: B 8 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.4521 (m-80) REVERT: B 14 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.4812 (tm-30) REVERT: B 123 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6862 (tp30) REVERT: B 297 ARG cc_start: 0.6698 (ttm170) cc_final: 0.6195 (mtt-85) REVERT: B 436 GLU cc_start: 0.5453 (OUTLIER) cc_final: 0.4332 (tp30) REVERT: B 468 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7470 (mp) REVERT: E 254 LEU cc_start: 0.6000 (OUTLIER) cc_final: 0.4703 (tt) REVERT: E 281 ILE cc_start: 0.2045 (OUTLIER) cc_final: 0.0421 (tt) REVERT: E 326 ARG cc_start: 0.4599 (OUTLIER) cc_final: 0.3641 (ttm110) outliers start: 97 outliers final: 50 residues processed: 199 average time/residue: 0.4145 time to fit residues: 91.2718 Evaluate side-chains 173 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 112 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 376 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 51 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 HIS ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.235927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.209172 restraints weight = 13904.167| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 2.16 r_work: 0.4225 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11726 Z= 0.202 Angle : 0.685 8.983 15906 Z= 0.358 Chirality : 0.045 0.193 1710 Planarity : 0.005 0.046 2032 Dihedral : 9.667 161.029 1688 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 7.11 % Allowed : 34.87 % Favored : 58.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.21), residues: 1384 helix: -0.21 (0.27), residues: 378 sheet: -2.08 (0.43), residues: 154 loop : -3.20 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 120 TYR 0.026 0.002 TYR B 398 PHE 0.020 0.002 PHE B 335 TRP 0.017 0.002 TRP E 378 HIS 0.007 0.001 HIS E 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (11726) covalent geometry : angle 0.68506 / 0.36 (15906) hydrogen bonds : bond 0.04445 / 2.98 ( 305) hydrogen bonds : angle 5.77050 / 4.28 ( 867) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 116 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 6 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.4433 (ttp-170) REVERT: A 14 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.4943 (tm-30) REVERT: A 255 GLU cc_start: 0.6885 (mp0) cc_final: 0.6179 (mp0) REVERT: A 297 ARG cc_start: 0.6577 (ttm170) cc_final: 0.6189 (mtt-85) REVERT: A 303 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7212 (mtt180) REVERT: B 8 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.4525 (m-80) REVERT: B 14 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.4744 (tm-30) REVERT: B 123 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6837 (tp30) REVERT: B 297 ARG cc_start: 0.6793 (ttm170) cc_final: 0.6207 (mtt-85) REVERT: B 436 GLU cc_start: 0.5514 (OUTLIER) cc_final: 0.4286 (tp30) REVERT: B 468 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7545 (mp) REVERT: E 254 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.4696 (tt) REVERT: E 281 ILE cc_start: 0.2159 (OUTLIER) cc_final: 0.0518 (tt) REVERT: E 326 ARG cc_start: 0.4518 (OUTLIER) cc_final: 0.3590 (ttm110) outliers start: 85 outliers final: 56 residues processed: 190 average time/residue: 0.4611 time to fit residues: 96.5261 Evaluate side-chains 178 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 113 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 402 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 HIS ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.239389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.211775 restraints weight = 14025.742| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 2.08 r_work: 0.4259 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11726 Z= 0.130 Angle : 0.616 8.425 15906 Z= 0.322 Chirality : 0.043 0.179 1710 Planarity : 0.004 0.044 2032 Dihedral : 9.516 159.228 1688 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 5.35 % Allowed : 36.71 % Favored : 57.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.20), residues: 1384 helix: -0.08 (0.27), residues: 376 sheet: -2.33 (0.43), residues: 134 loop : -3.11 (0.18), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 377 TYR 0.021 0.001 TYR B 398 PHE 0.011 0.001 PHE E 327 TRP 0.017 0.001 TRP E 378 HIS 0.026 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (11726) covalent geometry : angle 0.61618 / 0.32 (15906) hydrogen bonds : bond 0.03841 / 2.60 ( 305) hydrogen bonds : angle 5.56647 / 4.19 ( 867) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 116 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 6 ARG cc_start: 0.5750 (OUTLIER) cc_final: 0.4332 (ttp-170) REVERT: A 13 LEU cc_start: 0.5569 (OUTLIER) cc_final: 0.5079 (mp) REVERT: A 237 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6101 (tp) REVERT: A 255 GLU cc_start: 0.6867 (mp0) cc_final: 0.6143 (mp0) REVERT: A 303 ARG cc_start: 0.7538 (mtp85) cc_final: 0.7220 (mtt180) REVERT: B 8 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.4522 (m-80) REVERT: B 14 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.4732 (tm-30) REVERT: B 96 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6880 (mp) REVERT: B 468 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7504 (mp) REVERT: E 254 LEU cc_start: 0.5890 (OUTLIER) cc_final: 0.4694 (tt) REVERT: E 281 ILE cc_start: 0.2028 (OUTLIER) cc_final: 0.0441 (tt) REVERT: E 326 ARG cc_start: 0.4413 (OUTLIER) cc_final: 0.3492 (ttm110) outliers start: 64 outliers final: 43 residues processed: 172 average time/residue: 0.4405 time to fit residues: 83.9108 Evaluate side-chains 162 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 109 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 376 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 23 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 104 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 134 optimal weight: 0.0020 chunk 101 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.240589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.213476 restraints weight = 13971.587| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 2.06 r_work: 0.4275 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11726 Z= 0.125 Angle : 0.598 8.204 15906 Z= 0.312 Chirality : 0.042 0.184 1710 Planarity : 0.004 0.042 2032 Dihedral : 9.376 158.179 1688 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 5.69 % Allowed : 36.54 % Favored : 57.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.21), residues: 1384 helix: 0.00 (0.27), residues: 376 sheet: -2.30 (0.43), residues: 134 loop : -3.05 (0.18), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 249 TYR 0.017 0.001 TYR B 398 PHE 0.011 0.001 PHE B 335 TRP 0.014 0.001 TRP E 378 HIS 0.004 0.001 HIS E 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (11726) covalent geometry : angle 0.59817 / 0.31 (15906) hydrogen bonds : bond 0.03653 / 2.47 ( 305) hydrogen bonds : angle 5.41489 / 4.10 ( 867) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 113 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.5704 (OUTLIER) cc_final: 0.4317 (ttp-170) REVERT: A 13 LEU cc_start: 0.5720 (OUTLIER) cc_final: 0.5278 (mp) REVERT: A 237 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6103 (tp) REVERT: A 255 GLU cc_start: 0.6875 (mp0) cc_final: 0.6159 (mp0) REVERT: A 303 ARG cc_start: 0.7541 (mtp85) cc_final: 0.7184 (mmt180) REVERT: B 8 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.4419 (m-80) REVERT: B 14 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.4708 (tm-30) REVERT: B 96 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6891 (mp) REVERT: B 123 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6595 (tp30) REVERT: B 468 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7517 (mp) REVERT: E 254 LEU cc_start: 0.5851 (OUTLIER) cc_final: 0.4702 (tt) REVERT: E 281 ILE cc_start: 0.2054 (OUTLIER) cc_final: 0.1091 (mp) REVERT: E 289 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.7057 (m-80) REVERT: E 402 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6892 (mmm) outliers start: 68 outliers final: 42 residues processed: 172 average time/residue: 0.3967 time to fit residues: 75.9551 Evaluate side-chains 162 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 109 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 402 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 60 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.240009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.212694 restraints weight = 14109.827| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 2.07 r_work: 0.4271 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11726 Z= 0.138 Angle : 0.610 8.418 15906 Z= 0.317 Chirality : 0.043 0.191 1710 Planarity : 0.004 0.042 2032 Dihedral : 9.371 158.416 1688 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 5.02 % Allowed : 37.21 % Favored : 57.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.21), residues: 1384 helix: 0.02 (0.27), residues: 376 sheet: -2.26 (0.43), residues: 134 loop : -3.04 (0.18), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 374 TYR 0.019 0.001 TYR B 398 PHE 0.013 0.001 PHE B 335 TRP 0.014 0.001 TRP E 378 HIS 0.003 0.001 HIS D 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (11726) covalent geometry : angle 0.60994 / 0.32 (15906) hydrogen bonds : bond 0.03704 / 2.51 ( 305) hydrogen bonds : angle 5.41369 / 4.08 ( 867) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 111 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.5726 (OUTLIER) cc_final: 0.4343 (ttp-170) REVERT: A 13 LEU cc_start: 0.5556 (OUTLIER) cc_final: 0.5146 (mp) REVERT: A 14 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.4900 (tm-30) REVERT: A 255 GLU cc_start: 0.6887 (mp0) cc_final: 0.6164 (mp0) REVERT: A 303 ARG cc_start: 0.7530 (mtp85) cc_final: 0.7181 (mmt180) REVERT: B 8 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.4424 (m-80) REVERT: B 14 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.4726 (tm-30) REVERT: B 96 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6854 (mp) REVERT: B 123 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6620 (tp30) REVERT: B 468 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7496 (mp) REVERT: E 254 LEU cc_start: 0.5872 (OUTLIER) cc_final: 0.4721 (tt) REVERT: E 281 ILE cc_start: 0.2064 (OUTLIER) cc_final: 0.1079 (mp) REVERT: E 289 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.7003 (m-80) REVERT: E 402 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6900 (mmm) outliers start: 60 outliers final: 45 residues processed: 163 average time/residue: 0.4061 time to fit residues: 73.7242 Evaluate side-chains 164 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 108 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 402 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 59 optimal weight: 0.0030 chunk 125 optimal weight: 6.9990 chunk 43 optimal weight: 0.3980 chunk 71 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 82 optimal weight: 9.9990 chunk 51 optimal weight: 0.0010 chunk 137 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 380 ASN A 452 GLN ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.243294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.216786 restraints weight = 14168.500| |-----------------------------------------------------------------------------| r_work (start): 0.4422 rms_B_bonded: 2.07 r_work: 0.4305 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11726 Z= 0.109 Angle : 0.587 8.182 15906 Z= 0.306 Chirality : 0.042 0.157 1710 Planarity : 0.004 0.043 2032 Dihedral : 9.276 156.533 1688 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 4.43 % Allowed : 37.71 % Favored : 57.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.21), residues: 1384 helix: 0.10 (0.27), residues: 378 sheet: -2.19 (0.43), residues: 134 loop : -2.96 (0.18), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 249 TYR 0.017 0.001 TYR A 413 PHE 0.011 0.001 PHE A 81 TRP 0.014 0.001 TRP E 378 HIS 0.012 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (11726) covalent geometry : angle 0.58708 / 0.31 (15906) hydrogen bonds : bond 0.03421 / 2.34 ( 305) hydrogen bonds : angle 5.27602 / 4.03 ( 867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3161.74 seconds wall clock time: 54 minutes 56.80 seconds (3296.80 seconds total)