Starting phenix.real_space_refine on Sat Jul 4 09:52:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ttc_26114/07_2026/7ttc_26114_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ttc_26114/07_2026/7ttc_26114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ttc_26114/07_2026/7ttc_26114_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ttc_26114/07_2026/7ttc_26114_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ttc_26114/07_2026/7ttc_26114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ttc_26114/07_2026/7ttc_26114.map" } resolution = 3.6 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= 0.007 sd= 0.071 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 2 5.49 5 S 32 5.16 5 C 6441 2.51 5 N 1728 2.21 5 O 1996 1.98 5 H 9775 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19974 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 4853 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 11, 'TRANS': 315} Chain breaks: 8 Chain: "A" Number of atoms: 9259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 9259 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 23, 'TRANS': 576} Chain breaks: 3 Chain: "E" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1324 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Chain: "D" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3356 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 9, 'TRANS': 201} Chain: "C" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 676 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Chain: "P" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 462 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'TRANS': 27} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'K33': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.94, per 1000 atoms: 0.15 Number of scatterers: 19974 At special positions: 0 Unit cell: (105.234, 124.563, 137.449, 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 32 16.00 P 2 15.00 O 1996 8.00 N 1728 7.00 C 6441 6.00 H 9775 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS P1299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 534.3 milliseconds 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 24.7% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.515A pdb=" N ILE B 241 " --> pdb=" O SER B 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 216 through 232 Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 297 through 314 removed outlier: 3.560A pdb=" N ARG A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.541A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 392 removed outlier: 3.533A pdb=" N VAL A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.974A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'D' and resid 34 through 45 Processing helix chain 'D' and resid 47 through 58 Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.748A pdb=" N LEU D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.445A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.713A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.636A pdb=" N LEU D 215 " --> pdb=" O THR D 211 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.609A pdb=" N ARG D 223 " --> pdb=" O GLU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 76 through 80 Processing sheet with id=AA1, first strand: chain 'B' and resid 48 through 50 Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 118 removed outlier: 6.011A pdb=" N GLY B 114 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR B 123 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR B 116 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N HIS B 121 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 126 " --> pdb=" O GLN B 130 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.678A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 201 through 203 removed outlier: 5.777A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.649A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.633A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.558A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 179 through 183 removed outlier: 3.865A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.144A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY A 270 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.517A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 802 through 806 removed outlier: 3.897A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP A 614 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 445 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL P1272 " --> pdb=" O ILE P1268 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE P1268 " --> pdb=" O VAL P1272 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.564A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 34 removed outlier: 3.864A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 34 removed outlier: 6.823A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 100 " --> pdb=" O ASN E 96 " (cutoff:3.500A) 487 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9775 1.03 - 1.23: 786 1.23 - 1.43: 3805 1.43 - 1.63: 5763 1.63 - 1.83: 62 Bond restraints: 20191 Sorted by residual: bond pdb=" O40 K33 A 901 " pdb=" P41 K33 A 901 " ideal model delta sigma weight residual 1.749 1.656 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C19 K33 A 901 " pdb=" C20 K33 A 901 " ideal model delta sigma weight residual 1.523 1.615 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C21 K33 A 901 " pdb=" C22 K33 A 901 " ideal model delta sigma weight residual 1.523 1.615 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C30 K33 A 901 " pdb=" N32 K33 A 901 " ideal model delta sigma weight residual 1.344 1.430 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C20 K33 A 901 " pdb=" C21 K33 A 901 " ideal model delta sigma weight residual 1.525 1.608 -0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 20186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 34904 1.70 - 3.39: 1174 3.39 - 5.09: 136 5.09 - 6.78: 14 6.78 - 8.48: 8 Bond angle restraints: 36236 Sorted by residual: angle pdb=" N ASN A 594 " pdb=" CA ASN A 594 " pdb=" C ASN A 594 " ideal model delta sigma weight residual 107.67 115.72 -8.05 2.09e+00 2.29e-01 1.48e+01 angle pdb=" N ASN A 448 " pdb=" CA ASN A 448 " pdb=" C ASN A 448 " ideal model delta sigma weight residual 107.93 102.56 5.37 1.65e+00 3.67e-01 1.06e+01 angle pdb=" N GLY D 153 " pdb=" CA GLY D 153 " pdb=" C GLY D 153 " ideal model delta sigma weight residual 112.77 116.93 -4.16 1.28e+00 6.10e-01 1.06e+01 angle pdb=" CB ARG D 188 " pdb=" CG ARG D 188 " pdb=" CD ARG D 188 " ideal model delta sigma weight residual 111.30 118.69 -7.39 2.30e+00 1.89e-01 1.03e+01 angle pdb=" N PHE A 738 " pdb=" CA PHE A 738 " pdb=" C PHE A 738 " ideal model delta sigma weight residual 109.24 114.08 -4.84 1.51e+00 4.39e-01 1.03e+01 ... (remaining 36231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 9075 17.83 - 35.67: 354 35.67 - 53.50: 148 53.50 - 71.33: 53 71.33 - 89.17: 10 Dihedral angle restraints: 9640 sinusoidal: 5202 harmonic: 4438 Sorted by residual: dihedral pdb=" CA PRO A 326 " pdb=" C PRO A 326 " pdb=" N GLU A 327 " pdb=" CA GLU A 327 " ideal model delta harmonic sigma weight residual 180.00 158.65 21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA SER B 137 " pdb=" C SER B 137 " pdb=" N ASP B 138 " pdb=" CA ASP B 138 " ideal model delta harmonic sigma weight residual 180.00 159.84 20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLN D 224 " pdb=" C GLN D 224 " pdb=" N MET D 225 " pdb=" CA MET D 225 " ideal model delta harmonic sigma weight residual 180.00 160.03 19.97 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 9637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1324 0.081 - 0.161: 210 0.161 - 0.242: 5 0.242 - 0.322: 2 0.322 - 0.403: 2 Chirality restraints: 1543 Sorted by residual: chirality pdb=" C37 K33 A 901 " pdb=" C36 K33 A 901 " pdb=" C81 K33 A 901 " pdb=" O38 K33 A 901 " both_signs ideal model delta sigma weight residual False 2.44 2.85 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" C39 K33 A 901 " pdb=" C45 K33 A 901 " pdb=" O38 K33 A 901 " pdb=" O40 K33 A 901 " both_signs ideal model delta sigma weight residual False -2.05 -2.43 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C34 K33 A 901 " pdb=" C33 K33 A 901 " pdb=" O35 K33 A 901 " pdb=" O83 K33 A 901 " both_signs ideal model delta sigma weight residual False 2.20 2.50 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1540 not shown) Planarity restraints: 3073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 112 " -0.076 9.50e-02 1.11e+02 3.65e-02 1.62e+01 pdb=" NE ARG D 112 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG D 112 " -0.056 2.00e-02 2.50e+03 pdb=" NH1 ARG D 112 " 0.041 2.00e-02 2.50e+03 pdb=" NH2 ARG D 112 " 0.027 2.00e-02 2.50e+03 pdb="HH11 ARG D 112 " -0.012 2.00e-02 2.50e+03 pdb="HH12 ARG D 112 " -0.004 2.00e-02 2.50e+03 pdb="HH21 ARG D 112 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 112 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 547 " 0.071 9.50e-02 1.11e+02 3.48e-02 1.52e+01 pdb=" NE ARG A 547 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 547 " 0.055 2.00e-02 2.50e+03 pdb=" NH1 ARG A 547 " -0.040 2.00e-02 2.50e+03 pdb=" NH2 ARG A 547 " -0.026 2.00e-02 2.50e+03 pdb="HH11 ARG A 547 " 0.011 2.00e-02 2.50e+03 pdb="HH12 ARG A 547 " 0.005 2.00e-02 2.50e+03 pdb="HH21 ARG A 547 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 547 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 781 " 0.017 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C GLY A 781 " -0.057 2.00e-02 2.50e+03 pdb=" O GLY A 781 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO A 782 " 0.019 2.00e-02 2.50e+03 ... (remaining 3070 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 512 2.13 - 2.75: 36432 2.75 - 3.36: 51789 3.36 - 3.98: 68328 3.98 - 4.60: 107233 Nonbonded interactions: 264294 Sorted by model distance: nonbonded pdb=" HD1 HIS A 533 " pdb=" OD1 ASP A 568 " model vdw 1.512 2.450 nonbonded pdb=" O SER E 44 " pdb="HH12 ARG E 47 " model vdw 1.548 2.450 nonbonded pdb="HD22 ASN A 185 " pdb=" O PHE A 188 " model vdw 1.555 2.450 nonbonded pdb=" OD1 ASP D 93 " pdb="HH12 ARG D 112 " model vdw 1.557 2.450 nonbonded pdb=" OD2 ASP B 363 " pdb=" HH TYR B 388 " model vdw 1.568 2.450 ... (remaining 264289 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.100 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.190 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.010 0.093 10418 Z= 0.436 Angle : 0.937 8.481 14147 Z= 0.547 Chirality : 0.056 0.403 1543 Planarity : 0.006 0.080 1845 Dihedral : 11.657 89.166 3783 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.23), residues: 1262 helix: 0.39 (0.28), residues: 268 sheet: 1.00 (0.25), residues: 408 loop : 0.75 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.064 0.005 ARG D 112 TYR 0.030 0.004 TYR D 77 PHE 0.025 0.003 PHE A 791 TRP 0.025 0.004 TRP E 73 HIS 0.009 0.003 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00984 / 0.44 (10416) covalent geometry : angle 0.93619 / 0.55 (14143) SS BOND : bond 0.00714 / 0.34 ( 2) SS BOND : angle 2.92593 / 1.69 ( 4) hydrogen bonds : bond 0.12716 / 8.35 ( 483) hydrogen bonds : angle 6.81918 / 4.68 ( 1323) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 287 ASN cc_start: 0.8446 (m-40) cc_final: 0.8137 (t0) REVERT: B 296 ILE cc_start: 0.8561 (mt) cc_final: 0.8235 (mt) REVERT: B 305 VAL cc_start: 0.9081 (t) cc_final: 0.8842 (p) REVERT: B 306 MET cc_start: 0.6787 (ppp) cc_final: 0.6507 (ppp) REVERT: B 369 THR cc_start: 0.6527 (m) cc_final: 0.6143 (m) REVERT: A 276 ASN cc_start: 0.8187 (t0) cc_final: 0.7983 (t0) REVERT: A 357 ASN cc_start: 0.8436 (t0) cc_final: 0.8048 (t0) REVERT: D 111 MET cc_start: 0.8769 (mmm) cc_final: 0.8549 (tpt) REVERT: D 172 ASP cc_start: 0.8529 (t70) cc_final: 0.8229 (t0) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2484 time to fit residues: 100.6061 Evaluate side-chains 203 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P1271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.175126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.114612 restraints weight = 41369.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120570 restraints weight = 19395.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.124224 restraints weight = 12702.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.126325 restraints weight = 10063.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127576 restraints weight = 8860.985| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10418 Z= 0.124 Angle : 0.563 6.470 14147 Z= 0.308 Chirality : 0.044 0.150 1543 Planarity : 0.004 0.048 1845 Dihedral : 6.593 84.250 1478 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.74 % Allowed : 6.76 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.23), residues: 1262 helix: 1.64 (0.30), residues: 274 sheet: 0.56 (0.24), residues: 421 loop : 0.74 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 661 TYR 0.013 0.001 TYR D 222 PHE 0.019 0.001 PHE A 440 TRP 0.016 0.001 TRP A 546 HIS 0.003 0.001 HIS B 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10416) covalent geometry : angle 0.56318 / 0.31 (14143) SS BOND : bond 0.00448 / 0.21 ( 2) SS BOND : angle 0.73092 / 0.39 ( 4) hydrogen bonds : bond 0.05073 / 3.32 ( 483) hydrogen bonds : angle 5.52758 / 3.82 ( 1323) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 216 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 287 ASN cc_start: 0.8841 (m-40) cc_final: 0.8580 (t0) REVERT: B 296 ILE cc_start: 0.8586 (mt) cc_final: 0.8364 (mt) REVERT: B 305 VAL cc_start: 0.9022 (t) cc_final: 0.8793 (p) REVERT: B 306 MET cc_start: 0.6637 (ppp) cc_final: 0.6347 (ppp) REVERT: B 331 VAL cc_start: 0.7156 (p) cc_final: 0.6669 (m) REVERT: A 303 LYS cc_start: 0.8453 (tptp) cc_final: 0.8204 (tmtt) REVERT: A 357 ASN cc_start: 0.7873 (t0) cc_final: 0.7657 (t0) REVERT: A 738 PHE cc_start: 0.8757 (p90) cc_final: 0.8492 (p90) REVERT: D 172 ASP cc_start: 0.8595 (t70) cc_final: 0.8281 (t0) outliers start: 8 outliers final: 5 residues processed: 221 average time/residue: 0.2188 time to fit residues: 66.1391 Evaluate side-chains 188 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 183 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain D residue 164 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 264 ASN A 185 ASN A 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.173115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.114356 restraints weight = 40952.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.119331 restraints weight = 21797.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.122455 restraints weight = 15112.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.124232 restraints weight = 12260.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125206 restraints weight = 10915.740| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10418 Z= 0.160 Angle : 0.539 4.354 14147 Z= 0.292 Chirality : 0.043 0.146 1543 Planarity : 0.004 0.050 1845 Dihedral : 6.192 88.509 1478 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.57 % Allowed : 8.06 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.23), residues: 1262 helix: 1.59 (0.30), residues: 274 sheet: 0.13 (0.23), residues: 439 loop : 0.76 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 215 TYR 0.021 0.001 TYR B 345 PHE 0.017 0.001 PHE A 440 TRP 0.010 0.001 TRP A 745 HIS 0.002 0.001 HIS B 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (10416) covalent geometry : angle 0.53847 / 0.29 (14143) SS BOND : bond 0.00116 / 0.06 ( 2) SS BOND : angle 1.33341 / 0.62 ( 4) hydrogen bonds : bond 0.04705 / 3.08 ( 483) hydrogen bonds : angle 5.21588 / 3.62 ( 1323) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 MET cc_start: 0.8169 (tmm) cc_final: 0.7467 (tmm) REVERT: B 287 ASN cc_start: 0.8954 (m-40) cc_final: 0.8702 (t0) REVERT: B 296 ILE cc_start: 0.8651 (mt) cc_final: 0.8395 (mt) REVERT: B 306 MET cc_start: 0.6675 (ppp) cc_final: 0.6392 (ppp) REVERT: A 239 ASN cc_start: 0.7978 (t0) cc_final: 0.7305 (p0) REVERT: A 314 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8192 (mtm110) REVERT: A 777 MET cc_start: 0.7932 (mmm) cc_final: 0.7678 (mmp) REVERT: D 111 MET cc_start: 0.8955 (mmm) cc_final: 0.8609 (tpt) REVERT: D 172 ASP cc_start: 0.8615 (t70) cc_final: 0.8309 (t0) outliers start: 17 outliers final: 12 residues processed: 210 average time/residue: 0.2216 time to fit residues: 63.5327 Evaluate side-chains 199 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain P residue 1271 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 123 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 0.0070 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 186 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.172668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119022 restraints weight = 41286.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120220 restraints weight = 20351.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.120065 restraints weight = 15669.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121224 restraints weight = 15733.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121301 restraints weight = 13866.752| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10418 Z= 0.132 Angle : 0.511 7.241 14147 Z= 0.274 Chirality : 0.042 0.139 1543 Planarity : 0.004 0.039 1845 Dihedral : 6.289 85.226 1478 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.57 % Allowed : 9.07 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.23), residues: 1262 helix: 1.71 (0.31), residues: 274 sheet: 0.07 (0.23), residues: 438 loop : 0.68 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 661 TYR 0.017 0.001 TYR D 79 PHE 0.014 0.001 PHE A 440 TRP 0.008 0.001 TRP A 745 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (10416) covalent geometry : angle 0.51122 / 0.27 (14143) SS BOND : bond 0.00199 / 0.10 ( 2) SS BOND : angle 0.92820 / 0.46 ( 4) hydrogen bonds : bond 0.04302 / 2.84 ( 483) hydrogen bonds : angle 5.05795 / 3.51 ( 1323) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 MET cc_start: 0.8247 (tmm) cc_final: 0.7598 (tmm) REVERT: B 296 ILE cc_start: 0.8666 (mt) cc_final: 0.8411 (mt) REVERT: B 306 MET cc_start: 0.6600 (ppp) cc_final: 0.6297 (ppp) REVERT: A 239 ASN cc_start: 0.8009 (t0) cc_final: 0.7372 (p0) REVERT: A 650 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7673 (mm-30) REVERT: D 111 MET cc_start: 0.8958 (mmm) cc_final: 0.8606 (tpt) REVERT: D 172 ASP cc_start: 0.8390 (t70) cc_final: 0.8165 (t0) REVERT: P 1300 PHE cc_start: 0.8619 (m-80) cc_final: 0.8224 (m-10) outliers start: 17 outliers final: 15 residues processed: 208 average time/residue: 0.1938 time to fit residues: 56.0929 Evaluate side-chains 197 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain P residue 1271 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 35 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 73 optimal weight: 0.5980 chunk 21 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.170856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115256 restraints weight = 40846.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.117554 restraints weight = 21198.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118135 restraints weight = 14500.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118238 restraints weight = 13665.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119263 restraints weight = 13104.803| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10418 Z= 0.191 Angle : 0.523 5.213 14147 Z= 0.284 Chirality : 0.042 0.138 1543 Planarity : 0.004 0.041 1845 Dihedral : 6.313 83.415 1478 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.76 % Allowed : 9.35 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.23), residues: 1262 helix: 1.69 (0.31), residues: 274 sheet: -0.09 (0.23), residues: 436 loop : 0.54 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 661 TYR 0.013 0.001 TYR D 184 PHE 0.013 0.001 PHE A 440 TRP 0.009 0.001 TRP A 745 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (10416) covalent geometry : angle 0.52274 / 0.28 (14143) SS BOND : bond 0.00166 / 0.08 ( 2) SS BOND : angle 1.02727 / 0.50 ( 4) hydrogen bonds : bond 0.04557 / 2.99 ( 483) hydrogen bonds : angle 5.10524 / 3.53 ( 1323) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 LEU cc_start: 0.8028 (tp) cc_final: 0.7789 (tp) REVERT: B 146 LYS cc_start: 0.8691 (tptp) cc_final: 0.8440 (tptp) REVERT: B 226 MET cc_start: 0.8228 (tmm) cc_final: 0.7586 (tmm) REVERT: B 296 ILE cc_start: 0.8700 (mt) cc_final: 0.8431 (mt) REVERT: B 306 MET cc_start: 0.6606 (ppp) cc_final: 0.6254 (ppp) REVERT: A 239 ASN cc_start: 0.8073 (t0) cc_final: 0.7357 (p0) REVERT: A 314 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8169 (mtm110) REVERT: A 650 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7793 (mm-30) outliers start: 19 outliers final: 15 residues processed: 200 average time/residue: 0.2597 time to fit residues: 70.9600 Evaluate side-chains 197 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain P residue 1271 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 8 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 5 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.171434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.112416 restraints weight = 40954.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.117718 restraints weight = 20839.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121004 restraints weight = 14209.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.123000 restraints weight = 11447.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.123857 restraints weight = 10114.440| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10418 Z= 0.141 Angle : 0.494 5.420 14147 Z= 0.265 Chirality : 0.042 0.135 1543 Planarity : 0.004 0.042 1845 Dihedral : 6.183 82.404 1478 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.30 % Allowed : 10.46 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.23), residues: 1262 helix: 1.69 (0.31), residues: 280 sheet: -0.07 (0.23), residues: 430 loop : 0.45 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 661 TYR 0.013 0.001 TYR D 184 PHE 0.013 0.001 PHE A 440 TRP 0.008 0.001 TRP A 745 HIS 0.002 0.001 HIS B 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (10416) covalent geometry : angle 0.49381 / 0.26 (14143) SS BOND : bond 0.00150 / 0.07 ( 2) SS BOND : angle 0.81772 / 0.40 ( 4) hydrogen bonds : bond 0.04175 / 2.75 ( 483) hydrogen bonds : angle 4.92916 / 3.41 ( 1323) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 LEU cc_start: 0.7963 (tp) cc_final: 0.7715 (tp) REVERT: B 146 LYS cc_start: 0.8673 (tptp) cc_final: 0.8469 (tptp) REVERT: B 226 MET cc_start: 0.8290 (tmm) cc_final: 0.7700 (tmm) REVERT: B 296 ILE cc_start: 0.8650 (mt) cc_final: 0.8415 (mt) REVERT: A 239 ASN cc_start: 0.8144 (t0) cc_final: 0.7575 (p0) REVERT: A 650 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7721 (mm-30) outliers start: 14 outliers final: 13 residues processed: 199 average time/residue: 0.2117 time to fit residues: 57.2603 Evaluate side-chains 193 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 32 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.170544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.117492 restraints weight = 41238.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117715 restraints weight = 21994.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.118094 restraints weight = 15662.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.118301 restraints weight = 14462.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119103 restraints weight = 13727.904| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10418 Z= 0.156 Angle : 0.507 7.751 14147 Z= 0.270 Chirality : 0.042 0.134 1543 Planarity : 0.004 0.047 1845 Dihedral : 6.136 79.526 1478 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.57 % Allowed : 10.93 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1262 helix: 1.77 (0.31), residues: 275 sheet: -0.12 (0.23), residues: 430 loop : 0.37 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 661 TYR 0.013 0.001 TYR D 184 PHE 0.013 0.001 PHE P1300 TRP 0.008 0.001 TRP A 745 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (10416) covalent geometry : angle 0.50682 / 0.27 (14143) SS BOND : bond 0.00202 / 0.10 ( 2) SS BOND : angle 0.83143 / 0.40 ( 4) hydrogen bonds : bond 0.04179 / 2.76 ( 483) hydrogen bonds : angle 4.87556 / 3.36 ( 1323) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 LEU cc_start: 0.8022 (tp) cc_final: 0.7792 (tp) REVERT: B 226 MET cc_start: 0.8254 (tmm) cc_final: 0.7686 (tmm) REVERT: B 296 ILE cc_start: 0.8628 (mt) cc_final: 0.8392 (mt) REVERT: B 306 MET cc_start: 0.6499 (ppp) cc_final: 0.6213 (ppp) REVERT: B 329 SER cc_start: 0.9270 (p) cc_final: 0.9069 (t) REVERT: A 239 ASN cc_start: 0.8176 (t0) cc_final: 0.7572 (p0) REVERT: A 314 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8044 (mtm110) REVERT: A 650 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7791 (mm-30) outliers start: 17 outliers final: 14 residues processed: 201 average time/residue: 0.2473 time to fit residues: 67.3052 Evaluate side-chains 198 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain P residue 1271 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 96 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 60 optimal weight: 0.0170 chunk 16 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.170748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116920 restraints weight = 41284.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118301 restraints weight = 20124.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118356 restraints weight = 14866.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118610 restraints weight = 13952.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118851 restraints weight = 13360.128| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10418 Z= 0.146 Angle : 0.498 7.374 14147 Z= 0.266 Chirality : 0.042 0.135 1543 Planarity : 0.004 0.053 1845 Dihedral : 5.950 77.387 1478 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.57 % Allowed : 11.11 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.23), residues: 1262 helix: 1.73 (0.31), residues: 280 sheet: -0.07 (0.23), residues: 428 loop : 0.35 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 152 TYR 0.020 0.001 TYR B 333 PHE 0.013 0.001 PHE P1300 TRP 0.007 0.001 TRP A 745 HIS 0.002 0.001 HIS B 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (10416) covalent geometry : angle 0.49809 / 0.27 (14143) SS BOND : bond 0.00131 / 0.06 ( 2) SS BOND : angle 0.81266 / 0.39 ( 4) hydrogen bonds : bond 0.04067 / 2.68 ( 483) hydrogen bonds : angle 4.79660 / 3.31 ( 1323) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 LEU cc_start: 0.7998 (tp) cc_final: 0.7765 (tp) REVERT: B 226 MET cc_start: 0.8226 (tmm) cc_final: 0.7635 (tmm) REVERT: B 296 ILE cc_start: 0.8557 (mt) cc_final: 0.8310 (mt) REVERT: B 306 MET cc_start: 0.6453 (ppp) cc_final: 0.6162 (ppp) REVERT: A 239 ASN cc_start: 0.8209 (t0) cc_final: 0.7625 (p0) REVERT: A 650 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7781 (mm-30) REVERT: E 42 ASP cc_start: 0.7352 (m-30) cc_final: 0.7150 (m-30) outliers start: 17 outliers final: 14 residues processed: 202 average time/residue: 0.2390 time to fit residues: 66.0848 Evaluate side-chains 192 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 68 optimal weight: 0.0170 chunk 4 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.171095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116409 restraints weight = 40671.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.119376 restraints weight = 21559.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.120029 restraints weight = 15198.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120142 restraints weight = 13995.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.120501 restraints weight = 13618.840| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10418 Z= 0.134 Angle : 0.496 7.654 14147 Z= 0.263 Chirality : 0.042 0.132 1543 Planarity : 0.004 0.051 1845 Dihedral : 5.727 75.468 1478 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.30 % Allowed : 11.76 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.23), residues: 1262 helix: 1.91 (0.31), residues: 274 sheet: 0.03 (0.24), residues: 427 loop : 0.41 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 661 TYR 0.017 0.001 TYR B 333 PHE 0.013 0.001 PHE A 440 TRP 0.008 0.001 TRP A 546 HIS 0.002 0.001 HIS B 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (10416) covalent geometry : angle 0.49559 / 0.26 (14143) SS BOND : bond 0.00133 / 0.06 ( 2) SS BOND : angle 0.77355 / 0.38 ( 4) hydrogen bonds : bond 0.03903 / 2.57 ( 483) hydrogen bonds : angle 4.71299 / 3.24 ( 1323) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 MET cc_start: 0.8266 (tmm) cc_final: 0.7894 (tmm) REVERT: B 296 ILE cc_start: 0.8513 (mt) cc_final: 0.8276 (mt) REVERT: B 306 MET cc_start: 0.6437 (ppp) cc_final: 0.6163 (ppp) REVERT: A 239 ASN cc_start: 0.8184 (t0) cc_final: 0.7683 (p0) REVERT: A 650 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7723 (mm-30) outliers start: 14 outliers final: 14 residues processed: 196 average time/residue: 0.2370 time to fit residues: 62.9959 Evaluate side-chains 190 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 3 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 59 optimal weight: 0.0670 chunk 79 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 33 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.172496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114997 restraints weight = 40858.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120154 restraints weight = 21934.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.123394 restraints weight = 14323.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123179 restraints weight = 12601.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.123530 restraints weight = 12632.750| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10418 Z= 0.097 Angle : 0.481 7.817 14147 Z= 0.253 Chirality : 0.042 0.133 1543 Planarity : 0.004 0.053 1845 Dihedral : 5.483 77.544 1478 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.74 % Allowed : 12.69 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1262 helix: 1.93 (0.31), residues: 280 sheet: 0.14 (0.24), residues: 427 loop : 0.49 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 661 TYR 0.018 0.001 TYR B 333 PHE 0.016 0.001 PHE A 440 TRP 0.008 0.001 TRP A 546 HIS 0.005 0.000 HIS B 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (10416) covalent geometry : angle 0.48098 / 0.25 (14143) SS BOND : bond 0.00121 / 0.06 ( 2) SS BOND : angle 0.65392 / 0.32 ( 4) hydrogen bonds : bond 0.03503 / 2.32 ( 483) hydrogen bonds : angle 4.57373 / 3.15 ( 1323) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 183 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 MET cc_start: 0.8216 (tmm) cc_final: 0.7861 (tmm) REVERT: B 296 ILE cc_start: 0.8563 (mt) cc_final: 0.8313 (mt) REVERT: B 306 MET cc_start: 0.6291 (ppp) cc_final: 0.6004 (ppp) REVERT: A 239 ASN cc_start: 0.8238 (t0) cc_final: 0.7642 (p0) REVERT: A 650 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7698 (mm-30) REVERT: A 787 TYR cc_start: 0.7513 (t80) cc_final: 0.7161 (t80) outliers start: 8 outliers final: 8 residues processed: 189 average time/residue: 0.2217 time to fit residues: 57.1156 Evaluate side-chains 185 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 92 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 99 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.172279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.114663 restraints weight = 40868.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120163 restraints weight = 21966.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122640 restraints weight = 14510.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122404 restraints weight = 12477.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122933 restraints weight = 12781.333| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 10418 Z= 0.183 Angle : 0.808 59.198 14147 Z= 0.479 Chirality : 0.044 0.538 1543 Planarity : 0.004 0.052 1845 Dihedral : 5.477 77.580 1478 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.74 % Allowed : 12.78 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.24), residues: 1262 helix: 1.94 (0.31), residues: 280 sheet: 0.15 (0.24), residues: 427 loop : 0.49 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 97 TYR 0.016 0.001 TYR B 333 PHE 0.015 0.001 PHE A 440 TRP 0.008 0.001 TRP A 546 HIS 0.003 0.000 HIS B 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (10416) covalent geometry : angle 0.80795 / 0.48 (14143) SS BOND : bond 0.00186 / 0.09 ( 2) SS BOND : angle 0.66297 / 0.33 ( 4) hydrogen bonds : bond 0.03574 / 2.37 ( 483) hydrogen bonds : angle 4.57956 / 3.16 ( 1323) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3396.77 seconds wall clock time: 58 minutes 18.56 seconds (3498.56 seconds total)