Starting phenix.real_space_refine on Tue Jun 10 01:40:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsb_61769/06_2025/9jsb_61769.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsb_61769/06_2025/9jsb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jsb_61769/06_2025/9jsb_61769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsb_61769/06_2025/9jsb_61769.map" model { file = "/net/cci-nas-00/data/ceres_data/9jsb_61769/06_2025/9jsb_61769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsb_61769/06_2025/9jsb_61769.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.32, per 1000 atoms: 0.73 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: 2.90 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.15 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: 3.35 Time building geometry restraints manager: 3.28 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: 0.02 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 29.820 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:14.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 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= 0.187 Angle : 0.781 10.155 15906 Z= 0.422 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.002 TRP E 212 HIS 0.027 0.001 HIS E 273 PHE 0.031 0.002 PHE E 202 TYR 0.021 0.002 TYR A 398 ARG 0.008 0.001 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.18045 ( 305) hydrogen bonds : angle 8.02866 ( 867) covalent geometry : bond 0.00397 (11726) covalent geometry : angle 0.78116 (15906) *********************** 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 : 1.273 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: 1.0968 time to fit residues: 165.9678 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 : 1.173 ------------------------------------------------------------------------------- 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 116 optimal weight: 0.0570 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 80 optimal weight: 0.5980 chunk 125 optimal weight: 7.9990 overall best weight: 1.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 HIS E 352 HIS E 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.242499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.214739 restraints weight = 13736.277| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 2.06 r_work: 0.4295 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11726 Z= 0.181 Angle : 0.659 9.209 15906 Z= 0.342 Chirality : 0.044 0.148 1710 Planarity : 0.005 0.071 2032 Dihedral : 9.529 157.369 1692 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 5.77 % Allowed : 33.86 % Favored : 60.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.20), residues: 1384 helix: -0.47 (0.26), residues: 384 sheet: -2.43 (0.36), residues: 204 loop : -3.06 (0.18), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 212 HIS 0.008 0.001 HIS A 78 PHE 0.019 0.002 PHE B 335 TYR 0.021 0.002 TYR A 398 ARG 0.007 0.001 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.04764 ( 305) hydrogen bonds : angle 5.93422 ( 867) covalent geometry : bond 0.00422 (11726) covalent geometry : angle 0.65883 (15906) *********************** 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 191 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 122 time to evaluate : 1.309 Fit side-chains REVERT: A 58 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7938 (tttt) REVERT: A 255 GLU cc_start: 0.6805 (mp0) cc_final: 0.6181 (mp0) REVERT: A 303 ARG cc_start: 0.7580 (mtp85) cc_final: 0.7225 (mtt180) REVERT: A 436 GLU cc_start: 0.5501 (OUTLIER) cc_final: 0.5243 (tp30) REVERT: A 468 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7498 (mp) REVERT: D 237 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7112 (ttmm) REVERT: B 248 ARG cc_start: 0.5257 (OUTLIER) cc_final: 0.3626 (ppp-140) REVERT: B 436 GLU cc_start: 0.5387 (OUTLIER) cc_final: 0.5180 (tp30) REVERT: B 468 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7369 (mp) REVERT: E 254 LEU cc_start: 0.5754 (OUTLIER) cc_final: 0.4627 (tt) REVERT: E 349 TYR cc_start: 0.4667 (p90) cc_final: 0.4414 (p90) REVERT: E 377 MET cc_start: 0.4194 (mpp) cc_final: 0.3974 (mtp) outliers start: 69 outliers final: 25 residues processed: 177 average time/residue: 1.2260 time to fit residues: 235.3146 Evaluate side-chains 152 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 468 LEU 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 259 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain B residue 248 ARG Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 375 ILE 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 205 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 254 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 47 optimal weight: 6.9990 chunk 111 optimal weight: 0.0470 chunk 132 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 52 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN B 224 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.243254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.215801 restraints weight = 13924.814| |-----------------------------------------------------------------------------| r_work (start): 0.4419 rms_B_bonded: 2.09 r_work: 0.4296 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.1350 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= 0.131 Angle : 0.592 8.138 15906 Z= 0.306 Chirality : 0.042 0.134 1710 Planarity : 0.004 0.059 2032 Dihedral : 9.272 156.389 1689 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 5.18 % Allowed : 35.03 % Favored : 59.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.21), residues: 1384 helix: -0.03 (0.27), residues: 380 sheet: -1.63 (0.42), residues: 156 loop : -3.06 (0.18), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 212 HIS 0.006 0.001 HIS E 273 PHE 0.014 0.001 PHE B 335 TYR 0.020 0.001 TYR A 398 ARG 0.009 0.000 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 305) hydrogen bonds : angle 5.60915 ( 867) covalent geometry : bond 0.00307 (11726) covalent geometry : angle 0.59213 (15906) *********************** 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 183 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 121 time to evaluate : 1.299 Fit side-chains REVERT: A 58 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7928 (tttt) REVERT: A 255 GLU cc_start: 0.6798 (mp0) cc_final: 0.6201 (mp0) REVERT: A 303 ARG cc_start: 0.7542 (mtp85) cc_final: 0.7195 (mtt180) REVERT: A 436 GLU cc_start: 0.5441 (OUTLIER) cc_final: 0.5241 (tp30) REVERT: A 468 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7558 (mp) REVERT: D 237 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7174 (ttmm) REVERT: B 8 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.4727 (m-80) REVERT: B 248 ARG cc_start: 0.5212 (OUTLIER) cc_final: 0.3547 (ppp-140) REVERT: B 403 MET cc_start: 0.6526 (OUTLIER) cc_final: 0.5782 (mmm) REVERT: B 436 GLU cc_start: 0.5325 (OUTLIER) cc_final: 0.5118 (tp30) REVERT: B 468 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7367 (mp) REVERT: E 330 MET cc_start: 0.5789 (mpt) cc_final: 0.5477 (mpt) outliers start: 62 outliers final: 30 residues processed: 170 average time/residue: 1.0703 time to fit residues: 199.5674 Evaluate side-chains 149 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL 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 396 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 436 GLU 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 214 PHE Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 252 SER 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 248 ARG Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 340 SER 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 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 225 ILE Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 329 LEU 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 18 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 135 optimal weight: 0.0970 chunk 6 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 94 optimal weight: 0.0570 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 451 ASN B 452 GLN E 352 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.247511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.220777 restraints weight = 14018.965| |-----------------------------------------------------------------------------| r_work (start): 0.4453 rms_B_bonded: 2.10 r_work: 0.4336 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11726 Z= 0.102 Angle : 0.556 7.854 15906 Z= 0.287 Chirality : 0.040 0.151 1710 Planarity : 0.004 0.050 2032 Dihedral : 9.018 152.922 1689 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 5.43 % Allowed : 35.37 % Favored : 59.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.21), residues: 1384 helix: 0.20 (0.27), residues: 380 sheet: -2.14 (0.41), residues: 144 loop : -2.97 (0.18), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 212 HIS 0.004 0.001 HIS E 352 PHE 0.010 0.001 PHE B 335 TYR 0.019 0.001 TYR A 398 ARG 0.004 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 305) hydrogen bonds : angle 5.26901 ( 867) covalent geometry : bond 0.00238 (11726) covalent geometry : angle 0.55574 (15906) *********************** 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: 65 poor density : 128 time to evaluate : 1.320 Fit side-chains REVERT: A 6 ARG cc_start: 0.5089 (OUTLIER) cc_final: 0.4252 (ttp-170) REVERT: A 255 GLU cc_start: 0.6663 (mp0) cc_final: 0.6094 (mp0) REVERT: A 303 ARG cc_start: 0.7433 (mtp85) cc_final: 0.7133 (mtt180) REVERT: B 8 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.4699 (m-80) REVERT: B 14 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.4593 (tm-30) REVERT: B 248 ARG cc_start: 0.5131 (OUTLIER) cc_final: 0.3569 (ppp-140) REVERT: B 468 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7292 (mp) REVERT: E 330 MET cc_start: 0.5879 (mpt) cc_final: 0.5654 (mpt) outliers start: 65 outliers final: 30 residues processed: 181 average time/residue: 1.0509 time to fit residues: 208.8440 Evaluate side-chains 150 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 92 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 281 MET 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 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 252 SER Chi-restraints excluded: chain D residue 259 LEU 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 14 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 248 ARG Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 337 LEU 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 E residue 205 VAL Chi-restraints excluded: chain E residue 281 ILE 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 341 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 112 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 134 optimal weight: 0.0570 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 40 optimal weight: 0.0670 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN B 424 HIS ** E 273 HIS ** 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 = 0.4715 r_free = 0.4715 target = 0.248312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.222006 restraints weight = 13829.745| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 2.01 r_work: 0.4363 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11726 Z= 0.100 Angle : 0.546 7.110 15906 Z= 0.283 Chirality : 0.041 0.159 1710 Planarity : 0.004 0.044 2032 Dihedral : 8.913 153.343 1689 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 5.52 % Allowed : 36.04 % Favored : 58.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.21), residues: 1384 helix: 0.34 (0.27), residues: 380 sheet: -2.09 (0.42), residues: 144 loop : -2.88 (0.18), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 212 HIS 0.003 0.000 HIS E 352 PHE 0.009 0.001 PHE E 202 TYR 0.017 0.001 TYR B 398 ARG 0.006 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 305) hydrogen bonds : angle 5.15359 ( 867) covalent geometry : bond 0.00236 (11726) covalent geometry : angle 0.54579 (15906) *********************** 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 193 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 127 time to evaluate : 1.198 Fit side-chains REVERT: A 6 ARG cc_start: 0.4988 (OUTLIER) cc_final: 0.4407 (ttp-170) REVERT: A 303 ARG cc_start: 0.7471 (mtp85) cc_final: 0.7173 (mtt180) REVERT: A 432 GLN cc_start: 0.6050 (OUTLIER) cc_final: 0.5826 (pt0) REVERT: D 237 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7152 (ttmm) REVERT: D 255 LEU cc_start: 0.5951 (mp) cc_final: 0.5556 (mp) REVERT: B 8 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.4655 (m-80) REVERT: B 14 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.4601 (tm-30) REVERT: B 248 ARG cc_start: 0.5110 (OUTLIER) cc_final: 0.3629 (ppp-140) REVERT: B 403 MET cc_start: 0.6266 (OUTLIER) cc_final: 0.5765 (mmm) REVERT: E 254 LEU cc_start: 0.5638 (OUTLIER) cc_final: 0.4555 (tt) REVERT: E 330 MET cc_start: 0.5830 (mpt) cc_final: 0.5623 (mpt) outliers start: 66 outliers final: 32 residues processed: 184 average time/residue: 1.1292 time to fit residues: 228.0451 Evaluate side-chains 156 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 92 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 230 THR 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 432 GLN 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 214 PHE Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 252 SER 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 14 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 248 ARG 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 428 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 437 ILE 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 281 ILE Chi-restraints excluded: chain E residue 285 VAL 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 341 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 10 optimal weight: 0.1980 chunk 76 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 273 HIS E 215 HIS ** E 273 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.240491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.212537 restraints weight = 14029.325| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 2.08 r_work: 0.4278 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.1845 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= 0.178 Angle : 0.646 11.220 15906 Z= 0.330 Chirality : 0.044 0.161 1710 Planarity : 0.005 0.048 2032 Dihedral : 9.207 159.099 1689 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 7.02 % Allowed : 34.45 % Favored : 58.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.21), residues: 1384 helix: 0.14 (0.27), residues: 382 sheet: -2.10 (0.43), residues: 134 loop : -2.92 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 212 HIS 0.006 0.001 HIS D 273 PHE 0.020 0.002 PHE B 335 TYR 0.019 0.002 TYR E 349 ARG 0.006 0.000 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 305) hydrogen bonds : angle 5.43630 ( 867) covalent geometry : bond 0.00424 (11726) covalent geometry : angle 0.64638 (15906) *********************** 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 194 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 110 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: A 255 GLU cc_start: 0.6687 (mp0) cc_final: 0.6038 (mp0) REVERT: A 303 ARG cc_start: 0.7552 (mtp85) cc_final: 0.7235 (mtt180) REVERT: D 237 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7209 (ttmm) REVERT: D 333 GLN cc_start: 0.5127 (OUTLIER) cc_final: 0.4619 (mt0) REVERT: D 402 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6983 (mmm) REVERT: B 8 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.4455 (m-80) REVERT: B 14 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.4728 (tm-30) REVERT: B 127 ASP cc_start: 0.6245 (m-30) cc_final: 0.5754 (m-30) REVERT: B 248 ARG cc_start: 0.5210 (OUTLIER) cc_final: 0.3678 (ppp-140) REVERT: B 468 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7409 (mp) REVERT: E 254 LEU cc_start: 0.5790 (OUTLIER) cc_final: 0.4571 (tt) outliers start: 84 outliers final: 45 residues processed: 179 average time/residue: 1.2046 time to fit residues: 238.0884 Evaluate side-chains 154 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 101 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 58 LYS 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 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 281 MET 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 443 VAL 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 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 285 VAL Chi-restraints excluded: chain D residue 333 GLN 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 145 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 ASP 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 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 437 ILE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 477 ILE 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 336 LEU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 365 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 9 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN E 215 HIS ** E 273 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.236123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.206961 restraints weight = 14013.387| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 2.11 r_work: 0.4215 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11726 Z= 0.233 Angle : 0.741 12.005 15906 Z= 0.381 Chirality : 0.047 0.198 1710 Planarity : 0.006 0.049 2032 Dihedral : 9.663 161.722 1688 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 7.53 % Allowed : 33.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.21), residues: 1384 helix: -0.10 (0.27), residues: 380 sheet: -2.05 (0.42), residues: 154 loop : -3.11 (0.18), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 212 HIS 0.004 0.001 HIS A 21 PHE 0.024 0.002 PHE B 335 TYR 0.029 0.002 TYR B 398 ARG 0.008 0.001 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 305) hydrogen bonds : angle 5.78809 ( 867) covalent geometry : bond 0.00549 (11726) covalent geometry : angle 0.74057 (15906) *********************** 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 207 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 117 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.4818 (tm-30) REVERT: A 58 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7933 (tttt) REVERT: A 255 GLU cc_start: 0.6832 (mp0) cc_final: 0.6182 (mp0) REVERT: A 303 ARG cc_start: 0.7594 (mtp85) cc_final: 0.7283 (mtt180) REVERT: A 432 GLN cc_start: 0.6242 (OUTLIER) cc_final: 0.6042 (pt0) REVERT: A 468 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7572 (mp) REVERT: D 281 ILE cc_start: 0.2037 (OUTLIER) cc_final: 0.0270 (tt) REVERT: B 8 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.4493 (m-80) REVERT: B 14 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.4917 (tm-30) REVERT: B 297 ARG cc_start: 0.6839 (ttm170) cc_final: 0.6598 (mmt90) REVERT: B 468 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7533 (mp) REVERT: E 254 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.4540 (tt) REVERT: E 273 HIS cc_start: 0.6367 (t-90) cc_final: 0.6130 (t70) REVERT: E 281 ILE cc_start: 0.2042 (OUTLIER) cc_final: 0.0247 (tt) outliers start: 90 outliers final: 45 residues processed: 193 average time/residue: 1.1358 time to fit residues: 240.7585 Evaluate side-chains 166 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 111 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 58 LYS 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 261 VAL 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 397 LEU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 432 GLN 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 281 ILE Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 380 ARG 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 388 PHE 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 439 SER 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 28 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN E 215 HIS ** E 273 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.239399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.211111 restraints weight = 13952.421| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 2.08 r_work: 0.4260 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11726 Z= 0.149 Angle : 0.646 9.947 15906 Z= 0.333 Chirality : 0.043 0.164 1710 Planarity : 0.005 0.043 2032 Dihedral : 9.493 160.313 1688 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 5.85 % Allowed : 35.54 % Favored : 58.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.21), residues: 1384 helix: -0.01 (0.27), residues: 380 sheet: -1.88 (0.40), residues: 168 loop : -3.07 (0.18), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 378 HIS 0.004 0.001 HIS E 352 PHE 0.017 0.001 PHE B 335 TYR 0.022 0.002 TYR B 398 ARG 0.008 0.000 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 305) hydrogen bonds : angle 5.51097 ( 867) covalent geometry : bond 0.00352 (11726) covalent geometry : angle 0.64611 (15906) *********************** 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 186 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 116 time to evaluate : 1.362 Fit side-chains revert: symmetry clash REVERT: A 8 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.4472 (m-80) REVERT: A 14 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.4769 (tm-30) REVERT: A 237 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6113 (tp) REVERT: A 255 GLU cc_start: 0.6790 (mp0) cc_final: 0.6133 (mp0) REVERT: A 303 ARG cc_start: 0.7540 (mtp85) cc_final: 0.7189 (mmt180) REVERT: A 468 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7525 (mp) REVERT: D 255 LEU cc_start: 0.6130 (mp) cc_final: 0.5846 (mp) REVERT: D 281 ILE cc_start: 0.2051 (OUTLIER) cc_final: 0.0280 (tt) REVERT: B 8 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.4603 (m-80) REVERT: B 14 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.4796 (tm-30) REVERT: B 96 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6881 (mp) REVERT: B 127 ASP cc_start: 0.6365 (m-30) cc_final: 0.5952 (m-30) REVERT: B 436 GLU cc_start: 0.5421 (OUTLIER) cc_final: 0.4268 (tp30) REVERT: B 468 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7449 (mp) REVERT: E 254 LEU cc_start: 0.5860 (OUTLIER) cc_final: 0.4651 (tt) REVERT: E 281 ILE cc_start: 0.2177 (OUTLIER) cc_final: 0.0477 (tt) outliers start: 70 outliers final: 42 residues processed: 175 average time/residue: 0.9549 time to fit residues: 185.3318 Evaluate side-chains 162 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 108 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE 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 145 VAL Chi-restraints excluded: chain A residue 168 THR 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 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 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 14 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 96 ILE 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 337 LEU Chi-restraints excluded: chain B residue 340 SER 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 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 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 329 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 402 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 82 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 7 optimal weight: 0.0270 chunk 2 optimal weight: 4.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 215 HIS 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 = 0.4639 r_free = 0.4639 target = 0.239677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.211765 restraints weight = 14035.281| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 2.09 r_work: 0.4257 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11726 Z= 0.156 Angle : 0.650 12.076 15906 Z= 0.334 Chirality : 0.043 0.185 1710 Planarity : 0.005 0.043 2032 Dihedral : 9.461 160.398 1688 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 5.52 % Allowed : 36.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.21), residues: 1384 helix: -0.00 (0.27), residues: 382 sheet: -1.86 (0.40), residues: 168 loop : -3.03 (0.18), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 378 HIS 0.007 0.001 HIS E 273 PHE 0.017 0.002 PHE B 335 TYR 0.020 0.001 TYR B 398 ARG 0.007 0.000 ARG E 380 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 305) hydrogen bonds : angle 5.48319 ( 867) covalent geometry : bond 0.00371 (11726) covalent geometry : angle 0.65014 (15906) *********************** 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 174 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 108 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.4410 (m-80) REVERT: A 14 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.4783 (tm-30) REVERT: A 237 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6071 (tp) REVERT: A 255 GLU cc_start: 0.6869 (mp0) cc_final: 0.6197 (mp0) REVERT: A 303 ARG cc_start: 0.7549 (mtp85) cc_final: 0.7207 (mmt180) REVERT: A 468 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7537 (mp) REVERT: D 255 LEU cc_start: 0.6090 (mp) cc_final: 0.5782 (mp) REVERT: D 281 ILE cc_start: 0.2020 (OUTLIER) cc_final: 0.0251 (tt) REVERT: D 402 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6899 (mmm) REVERT: B 8 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.4455 (m-80) REVERT: B 14 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.4798 (tm-30) REVERT: B 96 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6839 (mp) REVERT: B 436 GLU cc_start: 0.5416 (OUTLIER) cc_final: 0.4207 (tp30) REVERT: B 468 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7419 (mp) REVERT: E 254 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.4616 (tt) REVERT: E 281 ILE cc_start: 0.2311 (OUTLIER) cc_final: 0.0617 (tt) outliers start: 66 outliers final: 44 residues processed: 164 average time/residue: 0.9575 time to fit residues: 174.2575 Evaluate side-chains 168 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 111 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE 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 145 VAL Chi-restraints excluded: chain A residue 168 THR 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 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 281 ILE Chi-restraints excluded: chain D residue 285 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 96 ILE 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 337 LEU Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 375 ILE 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 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 177 MET Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 215 HIS 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 329 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 365 LEU 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 118 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 67 optimal weight: 0.0370 chunk 70 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 GLN E 215 HIS E 273 HIS ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.243415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.216970 restraints weight = 14117.931| |-----------------------------------------------------------------------------| r_work (start): 0.4422 rms_B_bonded: 2.06 r_work: 0.4303 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11726 Z= 0.116 Angle : 0.616 10.680 15906 Z= 0.317 Chirality : 0.042 0.183 1710 Planarity : 0.004 0.055 2032 Dihedral : 9.292 157.633 1688 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 3.68 % Allowed : 37.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.21), residues: 1384 helix: 0.14 (0.27), residues: 382 sheet: -1.75 (0.41), residues: 168 loop : -2.91 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 212 HIS 0.012 0.001 HIS E 215 PHE 0.012 0.001 PHE A 59 TYR 0.017 0.001 TYR A 413 ARG 0.008 0.000 ARG E 380 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 305) hydrogen bonds : angle 5.28753 ( 867) covalent geometry : bond 0.00269 (11726) covalent geometry : angle 0.61573 (15906) ********************** 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 159 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.4533 (m-80) REVERT: A 255 GLU cc_start: 0.6654 (mp0) cc_final: 0.6225 (mp0) REVERT: A 303 ARG cc_start: 0.7486 (mtp85) cc_final: 0.7183 (mmt180) REVERT: A 468 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7523 (mp) REVERT: D 255 LEU cc_start: 0.5992 (mp) cc_final: 0.5692 (mp) REVERT: B 8 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.4550 (m-80) REVERT: B 14 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.4729 (tm-30) REVERT: B 468 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7425 (mp) REVERT: E 281 ILE cc_start: 0.2236 (OUTLIER) cc_final: 0.0608 (tt) outliers start: 44 outliers final: 31 residues processed: 154 average time/residue: 1.0436 time to fit residues: 178.2367 Evaluate side-chains 146 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE 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 209 VAL 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 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 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 337 LEU Chi-restraints excluded: chain B residue 375 ILE 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 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 281 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.241174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.213837 restraints weight = 13783.055| |-----------------------------------------------------------------------------| r_work (start): 0.4401 rms_B_bonded: 2.06 r_work: 0.4281 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.2237 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= 0.136 Angle : 0.619 7.814 15906 Z= 0.319 Chirality : 0.043 0.193 1710 Planarity : 0.004 0.042 2032 Dihedral : 9.284 158.611 1688 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 4.43 % Allowed : 36.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.21), residues: 1384 helix: 0.18 (0.27), residues: 382 sheet: -1.77 (0.41), residues: 168 loop : -2.92 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 378 HIS 0.007 0.001 HIS E 352 PHE 0.015 0.001 PHE B 335 TYR 0.015 0.001 TYR B 398 ARG 0.007 0.000 ARG E 380 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 305) hydrogen bonds : angle 5.30804 ( 867) covalent geometry : bond 0.00323 (11726) covalent geometry : angle 0.61863 (15906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7192.04 seconds wall clock time: 126 minutes 50.69 seconds (7610.69 seconds total)