Starting phenix.real_space_refine on Wed Sep 17 20:39:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsb_61769/09_2025/9jsb_61769.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsb_61769/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jsb_61769/09_2025/9jsb_61769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsb_61769/09_2025/9jsb_61769.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jsb_61769/09_2025/9jsb_61769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsb_61769/09_2025/9jsb_61769.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 40 5.16 5 C 7222 2.51 5 N 1996 2.21 5 O 2166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11436 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3819 Classifications: {'peptide': 483} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 456} Chain: "D" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1793 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain breaks: 3 Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'RNA': 5} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'RNA': 5} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "B" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3819 Classifications: {'peptide': 483} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 456} Chain: "E" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1793 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.71, per 1000 atoms: 0.24 Number of scatterers: 11436 At special positions: 0 Unit cell: (118.15, 97.75, 93.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 10 15.00 Mg 2 11.99 O 2166 8.00 N 1996 7.00 C 7222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 598.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 22 sheets defined 30.0% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 removed outlier: 3.736A pdb=" N GLU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 63 Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 117 through 138 removed outlier: 3.746A pdb=" N VAL A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 164 removed outlier: 3.943A pdb=" N LYS A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.591A pdb=" N THR A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 241 removed outlier: 3.957A pdb=" N THR A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 327 Processing helix chain 'A' and resid 343 through 355 Processing helix chain 'A' and resid 429 through 438 Processing helix chain 'A' and resid 455 through 468 removed outlier: 3.943A pdb=" N ALA A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 484 removed outlier: 3.558A pdb=" N LYS A 483 " --> pdb=" O ASP A 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 225 removed outlier: 3.610A pdb=" N GLU D 224 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE D 225 " --> pdb=" O CYS D 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 221 through 225' Processing helix chain 'D' and resid 235 through 240 removed outlier: 4.047A pdb=" N LEU D 239 " --> pdb=" O ASN D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 261 removed outlier: 3.669A pdb=" N GLN D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'B' and resid 23 through 31 removed outlier: 3.599A pdb=" N ALA B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 64 Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 117 through 137 removed outlier: 3.796A pdb=" N VAL B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 164 removed outlier: 3.538A pdb=" N ARG B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 190 Processing helix chain 'B' and resid 201 through 206 removed outlier: 3.597A pdb=" N ILE B 205 " --> pdb=" O TRP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 225 through 230 removed outlier: 3.512A pdb=" N THR B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 240 removed outlier: 3.901A pdb=" N THR B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 327 Processing helix chain 'B' and resid 343 through 355 Processing helix chain 'B' and resid 429 through 439 Processing helix chain 'B' and resid 455 through 468 removed outlier: 4.017A pdb=" N ALA B 461 " --> pdb=" O PRO B 457 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 484 removed outlier: 3.613A pdb=" N LYS B 483 " --> pdb=" O ASP B 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 231 removed outlier: 3.696A pdb=" N GLN E 230 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL E 231 " --> pdb=" O ILE E 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 227 through 231' Processing helix chain 'E' and resid 235 through 240 removed outlier: 4.325A pdb=" N LEU E 239 " --> pdb=" O ASN E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 261 removed outlier: 3.568A pdb=" N TYR E 261 " --> pdb=" O GLN E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 377 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 43 removed outlier: 3.569A pdb=" N ILE A 42 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 95 " --> pdb=" O ILE A 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48 removed outlier: 3.534A pdb=" N GLY A 48 " --> pdb=" O ALA A 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 150 removed outlier: 3.696A pdb=" N LEU A 150 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AA6, first strand: chain 'A' and resid 297 through 300 removed outlier: 7.514A pdb=" N HIS A 304 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 334 through 338 removed outlier: 6.694A pdb=" N VAL A 334 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL A 365 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE A 336 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AA9, first strand: chain 'D' and resid 324 through 328 removed outlier: 4.642A pdb=" N TRP D 334 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 336 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET D 402 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 179 through 181 Processing sheet with id=AB2, first strand: chain 'D' and resid 267 through 270 removed outlier: 3.639A pdb=" N ALA D 275 " --> pdb=" O ASP D 270 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 288 through 291 removed outlier: 3.895A pdb=" N TYR D 291 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR D 298 " --> pdb=" O TYR D 291 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.621A pdb=" N ARG B 6 " --> pdb=" O PHE B 388 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 388 " --> pdb=" O ARG B 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 13 through 15 Processing sheet with id=AB6, first strand: chain 'B' and resid 41 through 43 removed outlier: 5.928A pdb=" N ILE B 42 " --> pdb=" O GLU B 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AB8, first strand: chain 'B' and resid 288 through 289 removed outlier: 3.612A pdb=" N PHE B 282 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N CYS B 259 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU B 337 " --> pdb=" O CYS B 259 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL B 261 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL B 334 " --> pdb=" O ASP B 363 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL B 365 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 336 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL B 367 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LYS B 338 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLU B 369 " --> pdb=" O LYS B 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 297 through 300 removed outlier: 7.500A pdb=" N HIS B 304 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 168 through 169 Processing sheet with id=AC2, first strand: chain 'E' and resid 171 through 172 removed outlier: 3.762A pdb=" N MET E 402 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 267 through 270 removed outlier: 3.640A pdb=" N ALA E 275 " --> pdb=" O ASP E 270 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 289 through 291 305 hydrogen bonds defined for protein. 867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.15 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.630 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 20.380 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.47 (0.20), residues: 1384 helix: -1.18 (0.24), residues: 360 sheet: -2.01 (0.38), residues: 202 loop : -3.06 (0.18), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 249 TYR 0.021 0.002 TYR A 398 PHE 0.031 0.002 PHE E 202 TRP 0.020 0.002 TRP E 212 HIS 0.027 0.001 HIS E 273 Details of bonding type rmsd covalent geometry : bond 0.00397 (11726) covalent geometry : angle 0.78116 (15906) hydrogen bonds : bond 0.18045 ( 305) hydrogen bonds : angle 8.02866 ( 867) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.473 Fit side-chains REVERT: A 237 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6454 (tp) outliers start: 19 outliers final: 4 residues processed: 138 average time/residue: 0.5422 time to fit residues: 81.8699 Evaluate side-chains 115 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain E residue 205 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 HIS ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN A 451 ASN ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 HIS ** E 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 353 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.229378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.199509 restraints weight = 13869.616| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 2.09 r_work: 0.4147 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.102 11726 Z= 0.448 Angle : 1.031 17.470 15906 Z= 0.535 Chirality : 0.058 0.263 1710 Planarity : 0.009 0.079 2032 Dihedral : 10.564 167.633 1692 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.58 % Favored : 86.27 % Rotamer: Outliers : 9.87 % Allowed : 30.77 % Favored : 59.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.90 (0.19), residues: 1384 helix: -1.07 (0.25), residues: 380 sheet: -2.92 (0.36), residues: 202 loop : -3.43 (0.17), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 287 TYR 0.036 0.004 TYR A 398 PHE 0.043 0.004 PHE B 335 TRP 0.024 0.004 TRP E 212 HIS 0.013 0.002 HIS E 273 Details of bonding type rmsd covalent geometry : bond 0.01046 (11726) covalent geometry : angle 1.03115 (15906) hydrogen bonds : bond 0.06959 ( 305) hydrogen bonds : angle 6.89898 ( 867) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 134 time to evaluate : 0.382 Fit side-chains REVERT: A 6 ARG cc_start: 0.6045 (OUTLIER) cc_final: 0.4522 (ttp-170) REVERT: A 14 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.4784 (tm-30) REVERT: A 255 GLU cc_start: 0.6908 (mp0) cc_final: 0.6260 (mp0) REVERT: A 303 ARG cc_start: 0.7746 (mtp85) cc_final: 0.7385 (mtt180) REVERT: A 468 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7665 (mp) REVERT: A 482 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6561 (mmt180) REVERT: D 177 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6463 (tpp) REVERT: D 281 ILE cc_start: 0.2109 (OUTLIER) cc_final: 0.0254 (tt) REVERT: B 8 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.4640 (m-80) REVERT: B 248 ARG cc_start: 0.5654 (OUTLIER) cc_final: 0.5308 (ptt180) REVERT: B 385 ARG cc_start: 0.5744 (OUTLIER) cc_final: 0.2486 (ttt-90) REVERT: B 458 ILE cc_start: 0.6810 (mt) cc_final: 0.6426 (mm) REVERT: E 254 LEU cc_start: 0.6068 (OUTLIER) cc_final: 0.5720 (mp) REVERT: E 256 ARG cc_start: 0.5648 (OUTLIER) cc_final: 0.5362 (ttp80) REVERT: E 349 TYR cc_start: 0.4695 (p90) cc_final: 0.3987 (p90) outliers start: 118 outliers final: 57 residues processed: 229 average time/residue: 0.5716 time to fit residues: 142.3877 Evaluate side-chains 191 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 123 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 248 ARG Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 385 ARG 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 225 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 334 TRP Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 402 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 5 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 109 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN A 451 ASN ** 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 = 0.4644 r_free = 0.4644 target = 0.240353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.212777 restraints weight = 13997.057| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 2.05 r_work: 0.4274 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11726 Z= 0.126 Angle : 0.634 8.402 15906 Z= 0.330 Chirality : 0.042 0.164 1710 Planarity : 0.005 0.060 2032 Dihedral : 9.691 163.841 1691 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 5.27 % Allowed : 35.45 % Favored : 59.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.30 (0.20), residues: 1384 helix: -0.48 (0.26), residues: 378 sheet: -2.03 (0.40), residues: 156 loop : -3.24 (0.17), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 250 TYR 0.024 0.001 TYR A 398 PHE 0.013 0.001 PHE E 202 TRP 0.015 0.001 TRP D 378 HIS 0.006 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00289 (11726) covalent geometry : angle 0.63389 (15906) hydrogen bonds : bond 0.04156 ( 305) hydrogen bonds : angle 5.78410 ( 867) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 123 time to evaluate : 0.449 Fit side-chains REVERT: A 255 GLU cc_start: 0.6867 (mp0) cc_final: 0.6173 (mp0) REVERT: A 297 ARG cc_start: 0.6423 (ttm170) cc_final: 0.6101 (mtt-85) REVERT: A 303 ARG cc_start: 0.7471 (mtp85) cc_final: 0.7101 (mtt180) REVERT: B 8 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.4598 (m-80) REVERT: E 330 MET cc_start: 0.6074 (mpt) cc_final: 0.5672 (mpt) outliers start: 63 outliers final: 25 residues processed: 177 average time/residue: 0.5461 time to fit residues: 105.3689 Evaluate side-chains 138 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain D residue 213 SER 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 266 ASP Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 248 ARG Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 336 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 99 optimal weight: 0.0670 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 chunk 28 optimal weight: 0.0670 chunk 41 optimal weight: 0.4980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS B 452 GLN E 273 HIS E 352 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.242741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.215795 restraints weight = 13948.102| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 2.04 r_work: 0.4309 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.2004 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= 0.111 Angle : 0.582 10.993 15906 Z= 0.300 Chirality : 0.041 0.139 1710 Planarity : 0.004 0.050 2032 Dihedral : 9.253 161.890 1688 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 6.19 % Allowed : 33.95 % Favored : 59.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.20), residues: 1384 helix: -0.16 (0.27), residues: 378 sheet: -2.66 (0.38), residues: 162 loop : -3.05 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 6 TYR 0.019 0.001 TYR E 349 PHE 0.009 0.001 PHE B 81 TRP 0.013 0.001 TRP E 334 HIS 0.004 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00261 (11726) covalent geometry : angle 0.58156 (15906) hydrogen bonds : bond 0.03542 ( 305) hydrogen bonds : angle 5.42098 ( 867) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 124 time to evaluate : 0.485 Fit side-chains REVERT: A 6 ARG cc_start: 0.5381 (OUTLIER) cc_final: 0.4409 (ttp-170) REVERT: A 255 GLU cc_start: 0.6825 (mp0) cc_final: 0.6131 (mp0) REVERT: A 303 ARG cc_start: 0.7447 (mtp85) cc_final: 0.7069 (mtt180) REVERT: D 255 LEU cc_start: 0.5934 (mp) cc_final: 0.5564 (mp) REVERT: B 8 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.4406 (m-80) REVERT: B 14 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.4778 (tm-30) REVERT: B 436 GLU cc_start: 0.5140 (OUTLIER) cc_final: 0.3455 (tp30) REVERT: E 254 LEU cc_start: 0.5716 (OUTLIER) cc_final: 0.4565 (tt) REVERT: E 330 MET cc_start: 0.6062 (mpt) cc_final: 0.5774 (mpt) REVERT: E 380 ARG cc_start: 0.6249 (mmm-85) cc_final: 0.5936 (mmm-85) outliers start: 74 outliers final: 35 residues processed: 186 average time/residue: 0.4774 time to fit residues: 97.8059 Evaluate side-chains 152 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 261 VAL 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 468 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 396 LEU 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 205 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 376 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4617 r_free = 0.4617 target = 0.236659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.208467 restraints weight = 13851.434| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 2.03 r_work: 0.4229 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11726 Z= 0.197 Angle : 0.682 10.985 15906 Z= 0.351 Chirality : 0.045 0.175 1710 Planarity : 0.005 0.048 2032 Dihedral : 9.510 163.470 1688 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 7.86 % Allowed : 33.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.19 (0.21), residues: 1384 helix: -0.16 (0.27), residues: 380 sheet: -2.54 (0.38), residues: 182 loop : -3.16 (0.18), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 482 TYR 0.022 0.002 TYR B 398 PHE 0.022 0.002 PHE B 335 TRP 0.015 0.002 TRP E 212 HIS 0.005 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00468 (11726) covalent geometry : angle 0.68181 (15906) hydrogen bonds : bond 0.04487 ( 305) hydrogen bonds : angle 5.75748 ( 867) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 118 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 255 GLU cc_start: 0.6839 (mp0) cc_final: 0.6132 (mp0) REVERT: A 303 ARG cc_start: 0.7628 (mtp85) cc_final: 0.7299 (mtt180) REVERT: A 462 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6981 (tpp-160) REVERT: B 8 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.4509 (m-80) REVERT: B 14 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.4912 (tm-30) REVERT: B 115 GLU cc_start: 0.7023 (pt0) cc_final: 0.6112 (pt0) REVERT: B 297 ARG cc_start: 0.6749 (ttm170) cc_final: 0.6226 (mtt-85) REVERT: B 436 GLU cc_start: 0.5451 (OUTLIER) cc_final: 0.4379 (tp30) REVERT: E 254 LEU cc_start: 0.5894 (OUTLIER) cc_final: 0.4600 (tt) REVERT: E 281 ILE cc_start: 0.2093 (OUTLIER) cc_final: 0.0506 (tt) outliers start: 94 outliers final: 52 residues processed: 193 average time/residue: 0.5119 time to fit residues: 108.2672 Evaluate side-chains 170 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 112 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 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 205 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 402 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN A 432 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4589 r_free = 0.4589 target = 0.233667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.204451 restraints weight = 13949.437| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 2.09 r_work: 0.4194 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 11726 Z= 0.241 Angle : 0.737 12.273 15906 Z= 0.380 Chirality : 0.047 0.196 1710 Planarity : 0.006 0.048 2032 Dihedral : 9.736 163.450 1688 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 8.03 % Allowed : 34.11 % Favored : 57.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.27 (0.20), residues: 1384 helix: -0.34 (0.27), residues: 378 sheet: -2.16 (0.43), residues: 154 loop : -3.25 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 6 TYR 0.030 0.002 TYR B 398 PHE 0.025 0.002 PHE B 335 TRP 0.018 0.002 TRP E 212 HIS 0.005 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00568 (11726) covalent geometry : angle 0.73698 (15906) hydrogen bonds : bond 0.04827 ( 305) hydrogen bonds : angle 5.96845 ( 867) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 123 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 8 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.4469 (m-80) REVERT: A 13 LEU cc_start: 0.5723 (OUTLIER) cc_final: 0.5303 (mp) REVERT: A 14 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.4989 (tm-30) REVERT: A 255 GLU cc_start: 0.6924 (mp0) cc_final: 0.6215 (mp0) REVERT: A 297 ARG cc_start: 0.6538 (ttm170) cc_final: 0.6169 (mtt-85) REVERT: A 303 ARG cc_start: 0.7655 (mtp85) cc_final: 0.7299 (mtt180) REVERT: D 250 ARG cc_start: 0.5842 (OUTLIER) cc_final: 0.5539 (tpp80) REVERT: B 8 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.4523 (m-80) REVERT: B 14 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.4835 (tm-30) REVERT: B 297 ARG cc_start: 0.6780 (ttm170) cc_final: 0.6463 (mmt90) REVERT: B 436 GLU cc_start: 0.5608 (OUTLIER) cc_final: 0.4371 (tp30) REVERT: E 254 LEU cc_start: 0.5918 (OUTLIER) cc_final: 0.4538 (tt) REVERT: E 273 HIS cc_start: 0.6334 (t-90) cc_final: 0.6099 (t70) REVERT: E 281 ILE cc_start: 0.2406 (OUTLIER) cc_final: 0.1404 (mp) REVERT: E 289 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: E 326 ARG cc_start: 0.4727 (OUTLIER) cc_final: 0.3654 (ttm110) outliers start: 96 outliers final: 53 residues processed: 203 average time/residue: 0.4918 time to fit residues: 109.7046 Evaluate side-chains 179 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 115 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 462 ARG 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 213 SER Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain 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 168 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 402 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 51 optimal weight: 9.9990 chunk 53 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 131 optimal weight: 0.1980 chunk 117 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 122 optimal weight: 0.0070 chunk 86 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 452 GLN ** 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 = 0.4649 r_free = 0.4649 target = 0.240569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.215385 restraints weight = 13867.371| |-----------------------------------------------------------------------------| r_work (start): 0.4421 rms_B_bonded: 2.02 r_work: 0.4285 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 11726 Z= 0.121 Angle : 0.608 10.112 15906 Z= 0.315 Chirality : 0.042 0.160 1710 Planarity : 0.004 0.045 2032 Dihedral : 9.366 161.622 1688 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 5.85 % Allowed : 36.04 % Favored : 58.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.04 (0.21), residues: 1384 helix: -0.09 (0.27), residues: 376 sheet: -2.13 (0.42), residues: 156 loop : -3.10 (0.18), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 380 TYR 0.020 0.001 TYR B 398 PHE 0.011 0.001 PHE E 202 TRP 0.015 0.001 TRP E 378 HIS 0.003 0.001 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00282 (11726) covalent geometry : angle 0.60802 (15906) hydrogen bonds : bond 0.03617 ( 305) hydrogen bonds : angle 5.48007 ( 867) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 120 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.6929 (mp0) cc_final: 0.6232 (mp0) REVERT: A 303 ARG cc_start: 0.7465 (mtp85) cc_final: 0.7132 (mtt180) REVERT: B 8 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.4602 (m-80) REVERT: B 14 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.4808 (tm-30) REVERT: B 123 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6916 (tp30) REVERT: B 436 GLU cc_start: 0.5278 (OUTLIER) cc_final: 0.4047 (tp30) REVERT: E 289 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.7074 (m-80) outliers start: 70 outliers final: 41 residues processed: 181 average time/residue: 0.5075 time to fit residues: 100.8358 Evaluate side-chains 156 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 111 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 145 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 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 166 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 213 SER 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 50 SER Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 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 205 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 376 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN E 352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.239302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.212028 restraints weight = 13948.914| |-----------------------------------------------------------------------------| r_work (start): 0.4391 rms_B_bonded: 2.03 r_work: 0.4276 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.2428 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= 0.132 Angle : 0.613 10.759 15906 Z= 0.317 Chirality : 0.043 0.162 1710 Planarity : 0.005 0.044 2032 Dihedral : 9.308 161.411 1688 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 5.60 % Allowed : 36.45 % Favored : 57.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.98 (0.21), residues: 1384 helix: -0.05 (0.27), residues: 376 sheet: -2.11 (0.42), residues: 154 loop : -3.05 (0.18), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 380 TYR 0.017 0.001 TYR B 398 PHE 0.012 0.001 PHE B 335 TRP 0.015 0.001 TRP E 378 HIS 0.004 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00315 (11726) covalent geometry : angle 0.61318 (15906) hydrogen bonds : bond 0.03689 ( 305) hydrogen bonds : angle 5.44204 ( 867) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 113 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.5570 (OUTLIER) cc_final: 0.5089 (mp) REVERT: A 255 GLU cc_start: 0.6961 (mp0) cc_final: 0.6389 (mp0) REVERT: A 303 ARG cc_start: 0.7523 (mtp85) cc_final: 0.7202 (mtt180) REVERT: A 432 GLN cc_start: 0.6228 (OUTLIER) cc_final: 0.6017 (pt0) REVERT: A 462 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6868 (tpp-160) REVERT: B 8 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.4433 (m-80) REVERT: B 14 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.4780 (tm-30) REVERT: B 96 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6866 (mp) REVERT: B 123 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6877 (tp30) REVERT: B 436 GLU cc_start: 0.5348 (OUTLIER) cc_final: 0.4120 (tp30) REVERT: E 273 HIS cc_start: 0.6403 (t-90) cc_final: 0.6167 (t70) REVERT: E 289 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.7037 (m-80) outliers start: 67 outliers final: 47 residues processed: 171 average time/residue: 0.4984 time to fit residues: 93.8254 Evaluate side-chains 164 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 109 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 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 432 GLN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 213 SER 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 D residue 382 LEU Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 376 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 23 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 101 optimal weight: 0.0470 chunk 115 optimal weight: 1.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN ** 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 = 0.4621 r_free = 0.4621 target = 0.237273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.209564 restraints weight = 13849.419| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 2.01 r_work: 0.4248 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11726 Z= 0.180 Angle : 0.660 9.025 15906 Z= 0.341 Chirality : 0.045 0.174 1710 Planarity : 0.005 0.045 2032 Dihedral : 9.428 162.338 1688 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 5.85 % Allowed : 36.29 % Favored : 57.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.21), residues: 1384 helix: -0.08 (0.27), residues: 376 sheet: -2.17 (0.42), residues: 154 loop : -3.07 (0.18), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 380 TYR 0.021 0.002 TYR B 398 PHE 0.018 0.002 PHE B 335 TRP 0.015 0.002 TRP E 378 HIS 0.004 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00429 (11726) covalent geometry : angle 0.66032 (15906) hydrogen bonds : bond 0.04080 ( 305) hydrogen bonds : angle 5.57316 ( 867) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 111 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.5589 (OUTLIER) cc_final: 0.4411 (ttp-170) REVERT: A 13 LEU cc_start: 0.5663 (OUTLIER) cc_final: 0.5284 (mp) REVERT: A 255 GLU cc_start: 0.6906 (mp0) cc_final: 0.6415 (mp0) REVERT: A 303 ARG cc_start: 0.7580 (mtp85) cc_final: 0.7245 (mtt180) REVERT: A 432 GLN cc_start: 0.6290 (OUTLIER) cc_final: 0.6044 (pt0) REVERT: B 8 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.4428 (m-80) REVERT: B 14 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.4842 (tm-30) REVERT: B 96 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6859 (mp) REVERT: B 123 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6901 (tp30) REVERT: B 202 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6619 (mt-10) REVERT: B 436 GLU cc_start: 0.5502 (OUTLIER) cc_final: 0.4329 (tp30) REVERT: E 254 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.4642 (tt) REVERT: E 273 HIS cc_start: 0.6336 (t-90) cc_final: 0.6126 (t70) REVERT: E 289 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.6992 (m-80) outliers start: 70 outliers final: 51 residues processed: 171 average time/residue: 0.5336 time to fit residues: 100.0229 Evaluate side-chains 169 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 109 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 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 432 GLN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 402 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 60 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN E 352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.238409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.211172 restraints weight = 13996.328| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 2.01 r_work: 0.4269 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11726 Z= 0.134 Angle : 0.627 8.603 15906 Z= 0.324 Chirality : 0.043 0.175 1710 Planarity : 0.005 0.043 2032 Dihedral : 9.355 160.882 1688 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 5.10 % Allowed : 37.21 % Favored : 57.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.93 (0.21), residues: 1384 helix: 0.00 (0.27), residues: 376 sheet: -2.14 (0.42), residues: 154 loop : -3.02 (0.18), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 380 TYR 0.019 0.001 TYR B 398 PHE 0.012 0.001 PHE B 335 TRP 0.015 0.001 TRP E 378 HIS 0.007 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00316 (11726) covalent geometry : angle 0.62666 (15906) hydrogen bonds : bond 0.03749 ( 305) hydrogen bonds : angle 5.44650 ( 867) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 115 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.5458 (OUTLIER) cc_final: 0.4381 (ttp-170) REVERT: A 13 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5181 (mp) REVERT: A 255 GLU cc_start: 0.6879 (mp0) cc_final: 0.6402 (mp0) REVERT: A 303 ARG cc_start: 0.7527 (mtp85) cc_final: 0.7215 (mtt180) REVERT: B 8 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.4472 (m-80) REVERT: B 14 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.4815 (tm-30) REVERT: B 96 ILE cc_start: 0.7174 (OUTLIER) cc_final: 0.6905 (mp) REVERT: B 123 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6850 (tp30) REVERT: B 124 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6077 (pmm) REVERT: B 436 GLU cc_start: 0.5397 (OUTLIER) cc_final: 0.4189 (tp30) REVERT: E 254 LEU cc_start: 0.5847 (OUTLIER) cc_final: 0.4691 (tt) REVERT: E 273 HIS cc_start: 0.6378 (t-90) cc_final: 0.6173 (t70) REVERT: E 289 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7017 (m-80) outliers start: 61 outliers final: 49 residues processed: 170 average time/residue: 0.5086 time to fit residues: 95.0510 Evaluate side-chains 174 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 116 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 145 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 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 376 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 59 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 51 optimal weight: 0.0870 chunk 137 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 102 optimal weight: 4.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN 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 = 0.240949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.213608 restraints weight = 13927.504| |-----------------------------------------------------------------------------| r_work (start): 0.4402 rms_B_bonded: 2.09 r_work: 0.4285 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.2472 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= 0.118 Angle : 0.606 8.418 15906 Z= 0.313 Chirality : 0.042 0.171 1710 Planarity : 0.005 0.043 2032 Dihedral : 9.263 159.430 1688 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 5.02 % Allowed : 37.71 % Favored : 57.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.86 (0.21), residues: 1384 helix: 0.07 (0.27), residues: 378 sheet: -2.08 (0.42), residues: 154 loop : -2.98 (0.18), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 380 TYR 0.016 0.001 TYR B 398 PHE 0.012 0.001 PHE E 202 TRP 0.015 0.001 TRP E 378 HIS 0.010 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00276 (11726) covalent geometry : angle 0.60631 (15906) hydrogen bonds : bond 0.03531 ( 305) hydrogen bonds : angle 5.32214 ( 867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3443.30 seconds wall clock time: 59 minutes 42.82 seconds (3582.82 seconds total)