Starting phenix.real_space_refine on Thu Mar 5 07:25:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tt2_26108/03_2026/7tt2_26108.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tt2_26108/03_2026/7tt2_26108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tt2_26108/03_2026/7tt2_26108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tt2_26108/03_2026/7tt2_26108.map" model { file = "/net/cci-nas-00/data/ceres_data/7tt2_26108/03_2026/7tt2_26108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tt2_26108/03_2026/7tt2_26108.cif" } resolution = 4.2 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= 0.006 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 6551 2.51 5 N 1768 2.21 5 O 2031 1.98 5 H 9973 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20355 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3390 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "C" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 675 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1381 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "B" Number of atoms: 5199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5199 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 11, 'TRANS': 338} Chain breaks: 2 Chain: "A" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 9425 Classifications: {'peptide': 610} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 585} Chain breaks: 4 Chain: "P" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 285 Classifications: {'peptide': 18} Modifications used: {'COO': 1} Link IDs: {'TRANS': 17} Chain breaks: 1 Time building chain proxies: 3.47, per 1000 atoms: 0.17 Number of scatterers: 20355 At special positions: 0 Unit cell: (106.308, 127.785, 137.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 2031 8.00 N 1768 7.00 C 6551 6.00 H 9973 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=2.03 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: 1.63 Conformation dependent library (CDL) restraints added in 621.7 milliseconds 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2420 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 24.2% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 47 through 60 removed outlier: 3.558A pdb=" N LEU D 58 " --> pdb=" O GLN D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 removed outlier: 3.668A pdb=" N ALA D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.790A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.659A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.444A 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: 3.828A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.944A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.523A pdb=" N MET D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.569A pdb=" N ASN D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'E' and resid 23 through 27 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.669A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 232 removed outlier: 3.529A pdb=" N GLY A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.525A pdb=" N ILE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 313 Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.643A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 4.187A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 730 Processing sheet with id=AA1, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.790A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.779A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.891A pdb=" N GLY B 385 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 68 removed outlier: 5.569A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 111 through 117 removed outlier: 6.241A pdb=" N GLY B 114 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY B 125 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.734A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.848A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.823A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.650A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.781A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 179 through 183 removed outlier: 4.150A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR A 255 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL A 245 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR A 257 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR A 243 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN A 259 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.308A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 13.155A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 10.536A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 12.157A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.162A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.805A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.360A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 11.645A pdb=" N GLU A 420 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 802 through 806 removed outlier: 6.367A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 710 " --> pdb=" O TRP A 745 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 445 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS A 425 " --> pdb=" O GLN A 445 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.263A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1263 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: 4.77 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9973 1.03 - 1.23: 202 1.23 - 1.43: 4422 1.43 - 1.63: 5926 1.63 - 1.82: 60 Bond restraints: 20583 Sorted by residual: bond pdb=" C VAL A 444 " pdb=" N GLN A 445 " ideal model delta sigma weight residual 1.333 1.316 0.017 1.30e-02 5.92e+03 1.80e+00 bond pdb=" N ARG B 195 " pdb=" CA ARG B 195 " ideal model delta sigma weight residual 1.456 1.443 0.013 1.22e-02 6.72e+03 1.17e+00 bond pdb=" CB TRP A 376 " pdb=" CG TRP A 376 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.09e+00 bond pdb=" CA GLY B 169 " pdb=" C GLY B 169 " ideal model delta sigma weight residual 1.510 1.496 0.015 1.41e-02 5.03e+03 1.07e+00 bond pdb=" CG ARG A 366 " pdb=" CD ARG A 366 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.06e+00 ... (remaining 20578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 35860 1.80 - 3.60: 996 3.60 - 5.41: 113 5.41 - 7.21: 9 7.21 - 9.01: 3 Bond angle restraints: 36981 Sorted by residual: angle pdb=" N GLY B 214 " pdb=" CA GLY B 214 " pdb=" C GLY B 214 " ideal model delta sigma weight residual 115.32 108.79 6.53 1.48e+00 4.57e-01 1.95e+01 angle pdb=" N GLY A 424 " pdb=" CA GLY A 424 " pdb=" C GLY A 424 " ideal model delta sigma weight residual 113.18 104.17 9.01 2.37e+00 1.78e-01 1.44e+01 angle pdb=" C THR B 166 " pdb=" N SER B 167 " pdb=" CA SER B 167 " ideal model delta sigma weight residual 120.99 127.88 -6.89 1.86e+00 2.89e-01 1.37e+01 angle pdb=" N LEU B 192 " pdb=" CA LEU B 192 " pdb=" C LEU B 192 " ideal model delta sigma weight residual 110.80 118.52 -7.72 2.13e+00 2.20e-01 1.31e+01 angle pdb=" N GLY B 169 " pdb=" CA GLY B 169 " pdb=" C GLY B 169 " ideal model delta sigma weight residual 114.76 108.78 5.98 1.70e+00 3.46e-01 1.24e+01 ... (remaining 36976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 9244 17.34 - 34.69: 288 34.69 - 52.03: 173 52.03 - 69.38: 69 69.38 - 86.72: 10 Dihedral angle restraints: 9784 sinusoidal: 5247 harmonic: 4537 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -140.48 54.48 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CA PRO B 330 " pdb=" C PRO B 330 " pdb=" N VAL B 331 " pdb=" CA VAL B 331 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASP B 138 " pdb=" C ASP B 138 " pdb=" N GLY B 139 " pdb=" CA GLY B 139 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 9781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1044 0.042 - 0.084: 369 0.084 - 0.125: 120 0.125 - 0.167: 27 0.167 - 0.209: 3 Chirality restraints: 1563 Sorted by residual: chirality pdb=" CA ARG D 166 " pdb=" N ARG D 166 " pdb=" C ARG D 166 " pdb=" CB ARG D 166 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ARG D 61 " pdb=" N ARG D 61 " pdb=" C ARG D 61 " pdb=" CB ARG D 61 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.26e-01 chirality pdb=" CA HIS E 83 " pdb=" N HIS E 83 " pdb=" C HIS E 83 " pdb=" CB HIS E 83 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.19e-01 ... (remaining 1560 not shown) Planarity restraints: 3155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 34 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C GLU D 34 " 0.061 2.00e-02 2.50e+03 pdb=" O GLU D 34 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE D 35 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 166 " -0.016 2.00e-02 2.50e+03 3.38e-02 1.15e+01 pdb=" C THR B 166 " 0.058 2.00e-02 2.50e+03 pdb=" O THR B 166 " -0.023 2.00e-02 2.50e+03 pdb=" N SER B 167 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 86 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.13e+01 pdb=" C PRO D 86 " 0.058 2.00e-02 2.50e+03 pdb=" O PRO D 86 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU D 87 " -0.020 2.00e-02 2.50e+03 ... (remaining 3152 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 315 2.05 - 2.69: 30640 2.69 - 3.32: 55542 3.32 - 3.96: 72188 3.96 - 4.60: 111616 Nonbonded interactions: 270301 Sorted by model distance: nonbonded pdb=" O VAL E 27 " pdb=" HE2 HIS E 83 " model vdw 1.409 2.450 nonbonded pdb=" HD1 HIS A 533 " pdb=" OD1 ASP A 568 " model vdw 1.462 2.450 nonbonded pdb=" O TYR B 263 " pdb="HE22 GLN B 301 " model vdw 1.563 2.450 nonbonded pdb=" HH TYR E 28 " pdb=" OE2 GLU A 521 " model vdw 1.571 2.450 nonbonded pdb=" HH TYR A 674 " pdb=" OD2 ASP A 704 " model vdw 1.571 2.450 ... (remaining 270296 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.630 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10612 Z= 0.213 Angle : 0.913 9.008 14419 Z= 0.559 Chirality : 0.048 0.209 1563 Planarity : 0.005 0.073 1896 Dihedral : 10.679 86.722 3819 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.80 (0.22), residues: 1302 helix: 0.43 (0.28), residues: 264 sheet: 0.89 (0.24), residues: 404 loop : 0.51 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 661 TYR 0.019 0.002 TYR A 618 PHE 0.025 0.002 PHE A 354 TRP 0.022 0.003 TRP A 576 HIS 0.010 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00414 (10610) covalent geometry : angle 0.91266 (14415) SS BOND : bond 0.00350 ( 2) SS BOND : angle 2.26370 ( 4) hydrogen bonds : bond 0.12785 ( 462) hydrogen bonds : angle 7.07610 ( 1263) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 0.502 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 TYR cc_start: 0.8416 (m-80) cc_final: 0.7636 (m-10) REVERT: D 211 THR cc_start: 0.8519 (m) cc_final: 0.8293 (m) REVERT: E 26 VAL cc_start: 0.9114 (m) cc_final: 0.8756 (t) REVERT: E 28 TYR cc_start: 0.7452 (t80) cc_final: 0.7206 (t80) REVERT: B 62 ASN cc_start: 0.8721 (m-40) cc_final: 0.8085 (t0) REVERT: B 73 TYR cc_start: 0.8050 (m-80) cc_final: 0.7537 (m-80) REVERT: B 80 LEU cc_start: 0.8747 (tp) cc_final: 0.8462 (tt) REVERT: B 182 LYS cc_start: 0.9236 (mmmt) cc_final: 0.8582 (tttm) REVERT: B 287 ASN cc_start: 0.8540 (m-40) cc_final: 0.8081 (t0) REVERT: A 192 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8438 (tp30) REVERT: A 287 LEU cc_start: 0.9262 (mt) cc_final: 0.8741 (mm) REVERT: A 367 ARG cc_start: 0.8909 (mtm-85) cc_final: 0.8685 (mtm-85) REVERT: A 401 ASP cc_start: 0.8013 (t0) cc_final: 0.7635 (m-30) REVERT: A 738 PHE cc_start: 0.7138 (p90) cc_final: 0.6663 (p90) REVERT: A 776 TRP cc_start: 0.8501 (t60) cc_final: 0.7873 (t60) outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 0.2184 time to fit residues: 127.5578 Evaluate side-chains 264 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS A 280 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.166376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.127738 restraints weight = 56127.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135312 restraints weight = 38511.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.134032 restraints weight = 28825.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135696 restraints weight = 17672.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136404 restraints weight = 15507.806| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10612 Z= 0.257 Angle : 0.658 5.692 14419 Z= 0.373 Chirality : 0.044 0.172 1563 Planarity : 0.005 0.059 1896 Dihedral : 5.215 37.791 1453 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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 (0.22), residues: 1302 helix: 1.46 (0.30), residues: 267 sheet: 0.64 (0.24), residues: 411 loop : 0.33 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 304 TYR 0.022 0.002 TYR A 550 PHE 0.015 0.002 PHE P1296 TRP 0.014 0.002 TRP A 546 HIS 0.003 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00550 (10610) covalent geometry : angle 0.65791 (14415) SS BOND : bond 0.00499 ( 2) SS BOND : angle 1.12587 ( 4) hydrogen bonds : bond 0.05841 ( 462) hydrogen bonds : angle 6.18197 ( 1263) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.530 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: symmetry clash revert: symmetry clash REVERT: D 82 ASN cc_start: 0.8682 (t0) cc_final: 0.8295 (t0) REVERT: D 136 ASP cc_start: 0.8979 (t0) cc_final: 0.8617 (t0) REVERT: E 25 ARG cc_start: 0.8100 (ptp90) cc_final: 0.7752 (ptm160) REVERT: E 84 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7874 (mp0) REVERT: B 62 ASN cc_start: 0.8634 (m-40) cc_final: 0.8398 (t0) REVERT: B 283 LEU cc_start: 0.7488 (tp) cc_final: 0.7244 (pp) REVERT: B 297 TYR cc_start: 0.8069 (m-10) cc_final: 0.7765 (m-10) REVERT: B 388 TYR cc_start: 0.7175 (m-80) cc_final: 0.6955 (m-80) REVERT: A 303 LYS cc_start: 0.8591 (tttm) cc_final: 0.8156 (ttmm) REVERT: A 368 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7886 (mm-30) REVERT: A 401 ASP cc_start: 0.8342 (t0) cc_final: 0.7890 (m-30) REVERT: A 470 GLU cc_start: 0.7882 (tt0) cc_final: 0.7602 (tt0) REVERT: A 540 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7929 (mm-40) REVERT: A 738 PHE cc_start: 0.7521 (p90) cc_final: 0.6941 (p90) REVERT: A 768 MET cc_start: 0.7279 (ttp) cc_final: 0.6986 (ttm) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.2238 time to fit residues: 93.5149 Evaluate side-chains 234 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 39 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 129 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN ** E 83 HIS ** 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 = 0.4070 r_free = 0.4070 target = 0.169739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.130984 restraints weight = 56906.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.138040 restraints weight = 37820.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137695 restraints weight = 28142.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.139729 restraints weight = 17954.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.140168 restraints weight = 15677.517| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10612 Z= 0.125 Angle : 0.537 4.313 14419 Z= 0.299 Chirality : 0.043 0.156 1563 Planarity : 0.004 0.044 1896 Dihedral : 4.901 28.632 1453 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 0.82 (0.22), residues: 1302 helix: 1.78 (0.30), residues: 266 sheet: 0.50 (0.24), residues: 413 loop : 0.14 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 188 TYR 0.017 0.001 TYR A 550 PHE 0.011 0.001 PHE D 95 TRP 0.010 0.001 TRP B 93 HIS 0.008 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00259 (10610) covalent geometry : angle 0.53708 (14415) SS BOND : bond 0.00262 ( 2) SS BOND : angle 0.81553 ( 4) hydrogen bonds : bond 0.04776 ( 462) hydrogen bonds : angle 5.66596 ( 1263) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.504 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 TYR cc_start: 0.8821 (m-80) cc_final: 0.8138 (m-10) REVERT: D 136 ASP cc_start: 0.8959 (t0) cc_final: 0.8460 (t0) REVERT: D 187 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8130 (tm-30) REVERT: C 64 ASP cc_start: 0.8961 (t0) cc_final: 0.8613 (t0) REVERT: E 84 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7969 (mp0) REVERT: B 62 ASN cc_start: 0.8675 (m-40) cc_final: 0.8374 (t0) REVERT: A 368 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7920 (mm-30) REVERT: A 401 ASP cc_start: 0.8319 (t0) cc_final: 0.7810 (m-30) REVERT: A 606 ASN cc_start: 0.8563 (m110) cc_final: 0.8228 (m110) REVERT: A 743 THR cc_start: 0.8929 (t) cc_final: 0.8649 (m) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.2155 time to fit residues: 88.3443 Evaluate side-chains 240 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 106 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 49 optimal weight: 0.0670 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 264 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 = 0.4055 r_free = 0.4055 target = 0.168076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.128918 restraints weight = 56975.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.136678 restraints weight = 39730.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136754 restraints weight = 22999.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.137484 restraints weight = 17600.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139790 restraints weight = 15812.034| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10612 Z= 0.133 Angle : 0.517 5.074 14419 Z= 0.286 Chirality : 0.042 0.144 1563 Planarity : 0.004 0.046 1896 Dihedral : 4.720 20.027 1453 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: 1302 helix: 1.80 (0.30), residues: 273 sheet: 0.43 (0.24), residues: 411 loop : -0.11 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 304 TYR 0.015 0.001 TYR D 110 PHE 0.015 0.001 PHE A 648 TRP 0.009 0.001 TRP A 576 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00283 (10610) covalent geometry : angle 0.51627 (14415) SS BOND : bond 0.00632 ( 2) SS BOND : angle 1.86490 ( 4) hydrogen bonds : bond 0.04308 ( 462) hydrogen bonds : angle 5.45772 ( 1263) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.409 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: D 79 TYR cc_start: 0.8781 (m-80) cc_final: 0.7956 (m-10) REVERT: D 136 ASP cc_start: 0.8915 (t0) cc_final: 0.8397 (t0) REVERT: D 187 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8183 (tm-30) REVERT: C 49 GLU cc_start: 0.8236 (mp0) cc_final: 0.7962 (mm-30) REVERT: C 64 ASP cc_start: 0.8963 (t0) cc_final: 0.8515 (t0) REVERT: E 84 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8050 (mp0) REVERT: B 62 ASN cc_start: 0.8686 (m-40) cc_final: 0.8416 (t0) REVERT: A 367 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.8028 (mtm-85) REVERT: A 368 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7958 (mm-30) REVERT: A 401 ASP cc_start: 0.8272 (t0) cc_final: 0.7785 (m-30) REVERT: A 606 ASN cc_start: 0.8598 (m110) cc_final: 0.8173 (m110) REVERT: A 743 THR cc_start: 0.8908 (t) cc_final: 0.8587 (m) REVERT: A 776 TRP cc_start: 0.8785 (t60) cc_final: 0.8033 (t60) REVERT: A 789 GLN cc_start: 0.7845 (pt0) cc_final: 0.7541 (pt0) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.2140 time to fit residues: 84.2527 Evaluate side-chains 237 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 56 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 606 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.164700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126211 restraints weight = 56888.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130628 restraints weight = 40633.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131014 restraints weight = 31713.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.133672 restraints weight = 19375.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134251 restraints weight = 16291.844| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10612 Z= 0.186 Angle : 0.537 4.957 14419 Z= 0.300 Chirality : 0.042 0.153 1563 Planarity : 0.004 0.045 1896 Dihedral : 4.786 23.150 1453 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.09 % Allowed : 0.72 % Favored : 99.19 % 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: 0.30 (0.22), residues: 1302 helix: 1.55 (0.30), residues: 271 sheet: 0.25 (0.24), residues: 409 loop : -0.37 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 197 TYR 0.025 0.002 TYR A 550 PHE 0.014 0.001 PHE A 648 TRP 0.012 0.001 TRP A 576 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00399 (10610) covalent geometry : angle 0.53694 (14415) SS BOND : bond 0.01099 ( 2) SS BOND : angle 1.20682 ( 4) hydrogen bonds : bond 0.04448 ( 462) hydrogen bonds : angle 5.55736 ( 1263) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.527 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: D 79 TYR cc_start: 0.8861 (m-80) cc_final: 0.8260 (m-10) REVERT: D 82 ASN cc_start: 0.8578 (t0) cc_final: 0.8282 (t0) REVERT: D 136 ASP cc_start: 0.9049 (t0) cc_final: 0.8606 (t0) REVERT: D 187 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8228 (tm-30) REVERT: C 49 GLU cc_start: 0.8288 (mp0) cc_final: 0.8087 (mm-30) REVERT: C 64 ASP cc_start: 0.8986 (t0) cc_final: 0.8684 (t0) REVERT: E 84 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8123 (mp0) REVERT: B 62 ASN cc_start: 0.8734 (m-40) cc_final: 0.8501 (t0) REVERT: B 388 TYR cc_start: 0.7067 (m-80) cc_final: 0.6799 (m-80) REVERT: A 285 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 368 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8071 (mm-30) REVERT: A 401 ASP cc_start: 0.8341 (t0) cc_final: 0.7716 (m-30) REVERT: A 606 ASN cc_start: 0.8454 (m-40) cc_final: 0.8134 (m110) REVERT: A 776 TRP cc_start: 0.8883 (t60) cc_final: 0.8003 (t60) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.2280 time to fit residues: 85.5818 Evaluate side-chains 232 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 119 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.164767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126337 restraints weight = 56970.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.131092 restraints weight = 42674.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.131397 restraints weight = 31587.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.133473 restraints weight = 19643.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134322 restraints weight = 16965.513| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10612 Z= 0.155 Angle : 0.522 6.021 14419 Z= 0.288 Chirality : 0.042 0.157 1563 Planarity : 0.004 0.043 1896 Dihedral : 4.755 29.182 1453 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.09 % Allowed : 0.72 % Favored : 99.19 % 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: 0.25 (0.23), residues: 1302 helix: 1.67 (0.31), residues: 271 sheet: 0.17 (0.24), residues: 406 loop : -0.44 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 200 TYR 0.018 0.001 TYR A 550 PHE 0.022 0.001 PHE A 648 TRP 0.010 0.001 TRP A 739 HIS 0.002 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00334 (10610) covalent geometry : angle 0.52159 (14415) SS BOND : bond 0.00355 ( 2) SS BOND : angle 0.79476 ( 4) hydrogen bonds : bond 0.04236 ( 462) hydrogen bonds : angle 5.37544 ( 1263) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 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: 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: D 79 TYR cc_start: 0.8892 (m-80) cc_final: 0.8288 (m-10) REVERT: D 82 ASN cc_start: 0.8638 (t0) cc_final: 0.8327 (t0) REVERT: D 115 THR cc_start: 0.8906 (m) cc_final: 0.8683 (m) REVERT: D 136 ASP cc_start: 0.9018 (t0) cc_final: 0.8655 (t0) REVERT: D 187 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8282 (tm-30) REVERT: C 49 GLU cc_start: 0.8317 (mp0) cc_final: 0.8046 (mm-30) REVERT: C 64 ASP cc_start: 0.8959 (t0) cc_final: 0.8643 (t0) REVERT: E 84 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7955 (mp0) REVERT: B 62 ASN cc_start: 0.8917 (m-40) cc_final: 0.8657 (t0) REVERT: B 388 TYR cc_start: 0.7091 (m-80) cc_final: 0.6787 (m-80) REVERT: A 368 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8074 (mm-30) REVERT: A 369 MET cc_start: 0.8508 (mmm) cc_final: 0.8250 (mmm) REVERT: A 609 TYR cc_start: 0.8386 (p90) cc_final: 0.8025 (p90) REVERT: A 776 TRP cc_start: 0.8803 (t60) cc_final: 0.7891 (t60) outliers start: 1 outliers final: 0 residues processed: 265 average time/residue: 0.2358 time to fit residues: 86.7234 Evaluate side-chains 232 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 123 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS A 606 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.165483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.127126 restraints weight = 57317.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132475 restraints weight = 41914.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132316 restraints weight = 31287.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.134641 restraints weight = 19209.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135126 restraints weight = 16498.720| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10612 Z= 0.122 Angle : 0.497 4.215 14419 Z= 0.273 Chirality : 0.042 0.151 1563 Planarity : 0.004 0.041 1896 Dihedral : 4.635 32.952 1453 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.09 % Allowed : 0.54 % Favored : 99.37 % 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: 0.33 (0.23), residues: 1302 helix: 1.82 (0.31), residues: 273 sheet: 0.18 (0.24), residues: 406 loop : -0.41 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P1297 TYR 0.017 0.001 TYR A 550 PHE 0.011 0.001 PHE A 648 TRP 0.013 0.001 TRP D 48 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00263 (10610) covalent geometry : angle 0.49562 (14415) SS BOND : bond 0.00481 ( 2) SS BOND : angle 2.38297 ( 4) hydrogen bonds : bond 0.03926 ( 462) hydrogen bonds : angle 5.18474 ( 1263) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 0.474 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: D 79 TYR cc_start: 0.8825 (m-80) cc_final: 0.8188 (m-10) REVERT: D 109 MET cc_start: 0.8614 (mmm) cc_final: 0.8240 (mmt) REVERT: D 136 ASP cc_start: 0.8976 (t0) cc_final: 0.8582 (t0) REVERT: D 187 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8159 (tm-30) REVERT: C 49 GLU cc_start: 0.8323 (mp0) cc_final: 0.8080 (mm-30) REVERT: C 56 MET cc_start: 0.8650 (tpp) cc_final: 0.7855 (tpp) REVERT: C 57 ILE cc_start: 0.9110 (tp) cc_final: 0.8805 (tp) REVERT: C 64 ASP cc_start: 0.8968 (t0) cc_final: 0.8654 (t0) REVERT: E 53 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8875 (mm-40) REVERT: E 84 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7935 (mp0) REVERT: B 62 ASN cc_start: 0.8886 (m-40) cc_final: 0.8620 (t0) REVERT: B 163 LEU cc_start: 0.9262 (mt) cc_final: 0.8947 (mt) REVERT: B 388 TYR cc_start: 0.6915 (m-80) cc_final: 0.6575 (m-80) REVERT: A 285 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8081 (tm-30) REVERT: A 368 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8163 (mm-30) REVERT: A 369 MET cc_start: 0.8466 (mmm) cc_final: 0.8252 (mmm) REVERT: A 606 ASN cc_start: 0.8461 (m-40) cc_final: 0.8091 (m110) REVERT: A 651 ASN cc_start: 0.8791 (m-40) cc_final: 0.8467 (m-40) REVERT: A 776 TRP cc_start: 0.8822 (t60) cc_final: 0.7888 (t60) outliers start: 1 outliers final: 1 residues processed: 268 average time/residue: 0.2338 time to fit residues: 87.1232 Evaluate side-chains 244 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.161844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.122750 restraints weight = 54955.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126563 restraints weight = 39215.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126957 restraints weight = 31556.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.129613 restraints weight = 18943.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.130213 restraints weight = 15912.810| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 10612 Z= 0.257 Angle : 0.591 5.065 14419 Z= 0.331 Chirality : 0.043 0.161 1563 Planarity : 0.005 0.050 1896 Dihedral : 5.013 35.166 1453 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: -0.22 (0.23), residues: 1302 helix: 1.15 (0.30), residues: 274 sheet: -0.04 (0.25), residues: 415 loop : -0.76 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 197 TYR 0.022 0.002 TYR A 348 PHE 0.021 0.002 PHE A 648 TRP 0.019 0.002 TRP A 576 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00557 (10610) covalent geometry : angle 0.59004 (14415) SS BOND : bond 0.00408 ( 2) SS BOND : angle 2.12800 ( 4) hydrogen bonds : bond 0.04783 ( 462) hydrogen bonds : angle 5.64684 ( 1263) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.672 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: D 79 TYR cc_start: 0.8946 (m-80) cc_final: 0.8274 (m-10) REVERT: D 82 ASN cc_start: 0.8762 (t0) cc_final: 0.8382 (t0) REVERT: D 115 THR cc_start: 0.8946 (m) cc_final: 0.8744 (m) REVERT: D 136 ASP cc_start: 0.9091 (t0) cc_final: 0.8793 (t0) REVERT: D 187 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8332 (tm-30) REVERT: C 64 ASP cc_start: 0.8981 (t0) cc_final: 0.8568 (t0) REVERT: E 26 VAL cc_start: 0.9263 (t) cc_final: 0.9031 (p) REVERT: E 84 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8322 (mm-30) REVERT: B 62 ASN cc_start: 0.8936 (m-40) cc_final: 0.8675 (t0) REVERT: B 76 ASP cc_start: 0.5929 (t0) cc_final: 0.5676 (t0) REVERT: B 165 HIS cc_start: 0.8150 (t-90) cc_final: 0.7835 (t-90) REVERT: B 388 TYR cc_start: 0.7020 (m-80) cc_final: 0.6719 (m-80) REVERT: A 285 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8056 (tm-30) REVERT: A 368 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8148 (mm-30) REVERT: A 369 MET cc_start: 0.8510 (mmm) cc_final: 0.8282 (mmm) REVERT: A 651 ASN cc_start: 0.8949 (m-40) cc_final: 0.8645 (m-40) REVERT: A 776 TRP cc_start: 0.8899 (t60) cc_final: 0.7903 (t60) REVERT: P 1270 ASP cc_start: 0.7242 (t70) cc_final: 0.6795 (t0) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2402 time to fit residues: 86.1549 Evaluate side-chains 224 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 87 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 103 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.164813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125567 restraints weight = 54093.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.134566 restraints weight = 35387.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.132950 restraints weight = 23407.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.133788 restraints weight = 15181.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134111 restraints weight = 13672.702| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10612 Z= 0.119 Angle : 0.535 12.224 14419 Z= 0.292 Chirality : 0.044 0.322 1563 Planarity : 0.004 0.043 1896 Dihedral : 4.891 41.840 1453 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.23), residues: 1302 helix: 1.64 (0.31), residues: 275 sheet: 0.11 (0.25), residues: 397 loop : -0.67 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 83 TYR 0.016 0.001 TYR D 110 PHE 0.017 0.001 PHE A 648 TRP 0.009 0.001 TRP A 739 HIS 0.003 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00262 (10610) covalent geometry : angle 0.53214 (14415) SS BOND : bond 0.00364 ( 2) SS BOND : angle 3.49678 ( 4) hydrogen bonds : bond 0.04042 ( 462) hydrogen bonds : angle 5.24896 ( 1263) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.564 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: D 79 TYR cc_start: 0.8850 (m-80) cc_final: 0.8111 (m-10) REVERT: D 82 ASN cc_start: 0.8681 (t0) cc_final: 0.8352 (t0) REVERT: D 109 MET cc_start: 0.8512 (mmm) cc_final: 0.8067 (mmt) REVERT: D 115 THR cc_start: 0.8902 (m) cc_final: 0.8697 (m) REVERT: D 136 ASP cc_start: 0.8975 (t0) cc_final: 0.8740 (t0) REVERT: D 187 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8182 (tm-30) REVERT: C 56 MET cc_start: 0.8721 (tpp) cc_final: 0.7895 (tpp) REVERT: C 57 ILE cc_start: 0.9145 (tp) cc_final: 0.8828 (tp) REVERT: C 64 ASP cc_start: 0.8994 (t0) cc_final: 0.8729 (t0) REVERT: E 53 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8833 (mm-40) REVERT: E 84 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8341 (mm-30) REVERT: B 62 ASN cc_start: 0.8917 (m-40) cc_final: 0.8666 (t0) REVERT: B 165 HIS cc_start: 0.7862 (t-90) cc_final: 0.7582 (t-90) REVERT: B 388 TYR cc_start: 0.6851 (m-80) cc_final: 0.6514 (m-80) REVERT: A 368 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8122 (mm-30) REVERT: A 369 MET cc_start: 0.8495 (mmm) cc_final: 0.8230 (mmm) REVERT: A 420 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7280 (mt-10) REVERT: A 609 TYR cc_start: 0.8348 (p90) cc_final: 0.8124 (p90) REVERT: A 648 PHE cc_start: 0.8091 (p90) cc_final: 0.7570 (p90) REVERT: A 651 ASN cc_start: 0.8892 (m-40) cc_final: 0.8587 (m-40) REVERT: A 776 TRP cc_start: 0.8850 (t60) cc_final: 0.7859 (t60) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.2386 time to fit residues: 86.2987 Evaluate side-chains 228 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 91 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.165126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125710 restraints weight = 54747.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132369 restraints weight = 36720.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.131906 restraints weight = 27059.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.134087 restraints weight = 16624.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.134622 restraints weight = 14385.184| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10612 Z= 0.128 Angle : 0.521 9.533 14419 Z= 0.285 Chirality : 0.043 0.199 1563 Planarity : 0.004 0.060 1896 Dihedral : 4.867 50.178 1453 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.23), residues: 1302 helix: 1.67 (0.31), residues: 275 sheet: 0.10 (0.25), residues: 398 loop : -0.64 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 83 TYR 0.014 0.001 TYR D 184 PHE 0.016 0.001 PHE A 648 TRP 0.011 0.001 TRP D 48 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00282 (10610) covalent geometry : angle 0.51897 (14415) SS BOND : bond 0.00970 ( 2) SS BOND : angle 2.84091 ( 4) hydrogen bonds : bond 0.03906 ( 462) hydrogen bonds : angle 5.20345 ( 1263) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.525 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: D 79 TYR cc_start: 0.8870 (m-80) cc_final: 0.8272 (m-10) REVERT: D 82 ASN cc_start: 0.8699 (t0) cc_final: 0.8325 (t0) REVERT: D 115 THR cc_start: 0.8898 (m) cc_final: 0.8687 (m) REVERT: D 136 ASP cc_start: 0.8969 (t0) cc_final: 0.8664 (t0) REVERT: D 187 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8167 (tm-30) REVERT: C 64 ASP cc_start: 0.8984 (t0) cc_final: 0.8716 (t0) REVERT: E 84 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8314 (mm-30) REVERT: B 62 ASN cc_start: 0.8900 (m-40) cc_final: 0.8644 (t0) REVERT: B 84 LEU cc_start: 0.7632 (mm) cc_final: 0.7421 (mm) REVERT: B 165 HIS cc_start: 0.7851 (t-90) cc_final: 0.7583 (t-90) REVERT: B 388 TYR cc_start: 0.6814 (m-80) cc_final: 0.6467 (m-80) REVERT: A 368 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7975 (mm-30) REVERT: A 369 MET cc_start: 0.8464 (mmm) cc_final: 0.8228 (mmm) REVERT: A 372 MET cc_start: 0.8594 (mpp) cc_final: 0.8299 (mpp) REVERT: A 420 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7397 (mt-10) REVERT: A 606 ASN cc_start: 0.8450 (m-40) cc_final: 0.8184 (m110) REVERT: A 609 TYR cc_start: 0.8333 (p90) cc_final: 0.8089 (p90) REVERT: A 651 ASN cc_start: 0.8899 (m-40) cc_final: 0.8601 (m-40) REVERT: A 776 TRP cc_start: 0.8806 (t60) cc_final: 0.7822 (t60) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2363 time to fit residues: 84.0825 Evaluate side-chains 226 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 103 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 96 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.162391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123852 restraints weight = 57395.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126705 restraints weight = 43860.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127410 restraints weight = 35152.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.129943 restraints weight = 21307.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.130659 restraints weight = 18006.710| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10612 Z= 0.177 Angle : 0.545 6.762 14419 Z= 0.301 Chirality : 0.043 0.159 1563 Planarity : 0.004 0.044 1896 Dihedral : 4.997 57.304 1453 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.23), residues: 1302 helix: 1.45 (0.30), residues: 275 sheet: -0.08 (0.25), residues: 408 loop : -0.76 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 197 TYR 0.018 0.002 TYR D 184 PHE 0.021 0.001 PHE A 648 TRP 0.016 0.001 TRP A 576 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00386 (10610) covalent geometry : angle 0.54409 (14415) SS BOND : bond 0.00847 ( 2) SS BOND : angle 2.14320 ( 4) hydrogen bonds : bond 0.04184 ( 462) hydrogen bonds : angle 5.36434 ( 1263) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3289.44 seconds wall clock time: 56 minutes 43.31 seconds (3403.31 seconds total)