Starting phenix.real_space_refine on Tue Jun 17 20:23:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tt2_26108/06_2025/7tt2_26108.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tt2_26108/06_2025/7tt2_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_26108/06_2025/7tt2_26108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tt2_26108/06_2025/7tt2_26108.map" model { file = "/net/cci-nas-00/data/ceres_data/7tt2_26108/06_2025/7tt2_26108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tt2_26108/06_2025/7tt2_26108.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.15, per 1000 atoms: 0.45 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: 4.99 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.68 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: 7.73 Time building geometry restraints manager: 6.11 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: 0.970 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: 0.320 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.410 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.700 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.022 0.003 TRP A 576 HIS 0.010 0.001 HIS E 83 PHE 0.025 0.002 PHE A 354 TYR 0.019 0.002 TYR A 618 ARG 0.017 0.002 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.12785 ( 462) hydrogen bonds : angle 7.07610 ( 1263) SS BOND : bond 0.00350 ( 2) SS BOND : angle 2.26370 ( 4) covalent geometry : bond 0.00414 (10610) covalent geometry : angle 0.91266 (14415) *********************** 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 : 1.487 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: symmetry clash REVERT: D 79 TYR cc_start: 0.8416 (m-80) cc_final: 0.7634 (m-10) REVERT: D 211 THR cc_start: 0.8519 (m) cc_final: 0.8294 (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: 0.8051 (m-80) cc_final: 0.7538 (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: 0.8084 (t0) REVERT: A 192 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8439 (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: 0.7636 (m-30) REVERT: A 738 PHE cc_start: 0.7139 (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: 0.5281 time to fit residues: 312.5957 Evaluate side-chains 259 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** B 172 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.171535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133038 restraints weight = 56124.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.140797 restraints weight = 38440.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.140373 restraints weight = 25554.803| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3591 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= 0.145 Angle : 0.586 4.666 14419 Z= 0.328 Chirality : 0.044 0.169 1563 Planarity : 0.004 0.053 1896 Dihedral : 5.032 48.040 1453 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.22), residues: 1302 helix: 1.73 (0.30), residues: 267 sheet: 0.80 (0.24), residues: 410 loop : 0.52 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 546 HIS 0.004 0.001 HIS E 83 PHE 0.018 0.001 PHE A 785 TYR 0.025 0.002 TYR A 550 ARG 0.005 0.001 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.05420 ( 462) hydrogen bonds : angle 5.88454 ( 1263) SS BOND : bond 0.00333 ( 2) SS BOND : angle 1.21037 ( 4) covalent geometry : bond 0.00300 (10610) covalent geometry : angle 0.58548 (14415) *********************** 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 317 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.617 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 79 TYR cc_start: 0.8811 (m-80) cc_final: 0.7891 (m-10) REVERT: D 134 ASP cc_start: 0.8616 (m-30) cc_final: 0.8392 (m-30) REVERT: D 136 ASP cc_start: 0.8775 (t0) cc_final: 0.8287 (t0) REVERT: E 28 TYR cc_start: 0.7585 (t80) cc_final: 0.7384 (t80) REVERT: E 84 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7645 (mp0) REVERT: B 62 ASN cc_start: 0.8530 (m-40) cc_final: 0.8294 (t0) REVERT: B 270 LEU cc_start: 0.8358 (mp) cc_final: 0.8155 (mp) REVERT: B 287 ASN cc_start: 0.8532 (m-40) cc_final: 0.8134 (t0) REVERT: B 297 TYR cc_start: 0.7988 (m-10) cc_final: 0.7737 (m-10) REVERT: B 306 MET cc_start: 0.5775 (mtp) cc_final: 0.5344 (mtp) REVERT: A 368 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7846 (mm-30) REVERT: A 371 GLN cc_start: 0.7968 (tp40) cc_final: 0.7748 (tp-100) REVERT: A 401 ASP cc_start: 0.8182 (t0) cc_final: 0.7827 (m-30) REVERT: A 768 MET cc_start: 0.7120 (ttp) cc_final: 0.6873 (ttm) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.4918 time to fit residues: 216.7823 Evaluate side-chains 248 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 99 optimal weight: 3.9990 chunk 123 optimal weight: 0.0170 chunk 104 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- 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** ** B 266 ASN ** 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 = 0.4082 r_free = 0.4082 target = 0.170551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131786 restraints weight = 55893.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.134685 restraints weight = 35890.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139645 restraints weight = 22556.185| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10612 Z= 0.126 Angle : 0.524 4.942 14419 Z= 0.292 Chirality : 0.042 0.155 1563 Planarity : 0.004 0.046 1896 Dihedral : 4.790 36.186 1453 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.22), residues: 1302 helix: 1.89 (0.30), residues: 266 sheet: 0.58 (0.24), residues: 419 loop : 0.30 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 93 HIS 0.004 0.001 HIS E 83 PHE 0.011 0.001 PHE A 652 TYR 0.035 0.001 TYR A 550 ARG 0.004 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 462) hydrogen bonds : angle 5.56688 ( 1263) SS BOND : bond 0.00272 ( 2) SS BOND : angle 0.84422 ( 4) covalent geometry : bond 0.00263 (10610) covalent geometry : angle 0.52435 (14415) *********************** 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 304 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.722 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: 0.8786 (m-80) cc_final: 0.8115 (m-10) REVERT: D 115 THR cc_start: 0.8961 (m) cc_final: 0.8755 (m) REVERT: D 136 ASP cc_start: 0.8840 (t0) cc_final: 0.8248 (t0) REVERT: D 187 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8100 (tm-30) REVERT: C 64 ASP cc_start: 0.8838 (t0) cc_final: 0.8594 (t0) REVERT: E 84 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7970 (mp0) REVERT: B 62 ASN cc_start: 0.8600 (m-40) cc_final: 0.8317 (t0) REVERT: B 132 TYR cc_start: 0.8440 (m-80) cc_final: 0.7610 (m-10) REVERT: A 368 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7802 (mm-30) REVERT: A 401 ASP cc_start: 0.8153 (t0) cc_final: 0.7849 (m-30) REVERT: A 635 TRP cc_start: 0.7995 (m-90) cc_final: 0.7488 (m-10) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.4957 time to fit residues: 211.6091 Evaluate side-chains 241 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 128 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 129 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.169634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130817 restraints weight = 57346.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.138288 restraints weight = 40464.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138100 restraints weight = 25033.789| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10612 Z= 0.137 Angle : 0.516 4.935 14419 Z= 0.285 Chirality : 0.042 0.153 1563 Planarity : 0.004 0.045 1896 Dihedral : 4.638 23.349 1453 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.23), residues: 1302 helix: 1.85 (0.30), residues: 273 sheet: 0.52 (0.24), residues: 417 loop : 0.01 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 576 HIS 0.003 0.001 HIS E 83 PHE 0.013 0.001 PHE A 648 TYR 0.017 0.001 TYR A 550 ARG 0.003 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 462) hydrogen bonds : angle 5.35543 ( 1263) SS BOND : bond 0.00715 ( 2) SS BOND : angle 1.88143 ( 4) covalent geometry : bond 0.00293 (10610) covalent geometry : angle 0.51554 (14415) *********************** 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 286 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.545 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: 0.8835 (m-80) cc_final: 0.7974 (m-10) REVERT: D 136 ASP cc_start: 0.8905 (t0) cc_final: 0.8318 (t0) REVERT: D 187 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8174 (tm-30) REVERT: C 64 ASP cc_start: 0.8935 (t0) cc_final: 0.8508 (t0) REVERT: E 84 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8042 (mp0) REVERT: B 62 ASN cc_start: 0.8588 (m-40) cc_final: 0.8348 (t0) REVERT: B 221 MET cc_start: 0.7697 (mtp) cc_final: 0.7477 (mtp) REVERT: A 368 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7894 (mm-30) REVERT: A 401 ASP cc_start: 0.8111 (t0) cc_final: 0.7734 (m-30) REVERT: A 470 GLU cc_start: 0.7714 (tt0) cc_final: 0.7415 (tt0) REVERT: A 545 MET cc_start: 0.8767 (mtp) cc_final: 0.8550 (mtm) REVERT: A 606 ASN cc_start: 0.8542 (m110) cc_final: 0.8207 (m110) REVERT: A 635 TRP cc_start: 0.8009 (m-90) cc_final: 0.7382 (m100) REVERT: A 768 MET cc_start: 0.7405 (ttp) cc_final: 0.7010 (ttm) REVERT: A 776 TRP cc_start: 0.8793 (t60) cc_final: 0.8045 (t60) REVERT: A 789 GLN cc_start: 0.7824 (pt0) cc_final: 0.7556 (pt0) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.4867 time to fit residues: 193.9098 Evaluate side-chains 238 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 129 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.169670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130684 restraints weight = 56596.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136539 restraints weight = 40828.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136705 restraints weight = 28679.738| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10612 Z= 0.116 Angle : 0.492 3.960 14419 Z= 0.269 Chirality : 0.042 0.162 1563 Planarity : 0.004 0.041 1896 Dihedral : 4.516 17.507 1453 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1302 helix: 1.94 (0.30), residues: 273 sheet: 0.48 (0.24), residues: 413 loop : -0.10 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 576 HIS 0.005 0.001 HIS E 83 PHE 0.016 0.001 PHE A 648 TYR 0.014 0.001 TYR A 550 ARG 0.003 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 462) hydrogen bonds : angle 5.19319 ( 1263) SS BOND : bond 0.00301 ( 2) SS BOND : angle 1.10162 ( 4) covalent geometry : bond 0.00248 (10610) covalent geometry : angle 0.49160 (14415) *********************** 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 276 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 1.552 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: 0.8831 (m-80) cc_final: 0.8202 (m-10) REVERT: D 115 THR cc_start: 0.8881 (m) cc_final: 0.8680 (m) REVERT: D 136 ASP cc_start: 0.8874 (t0) cc_final: 0.8326 (t0) REVERT: D 187 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8161 (tm-30) REVERT: C 49 GLU cc_start: 0.8324 (mp0) cc_final: 0.8003 (mm-30) REVERT: C 56 MET cc_start: 0.8620 (tpp) cc_final: 0.7968 (tpp) REVERT: C 57 ILE cc_start: 0.9091 (tp) cc_final: 0.8787 (tp) REVERT: C 64 ASP cc_start: 0.8898 (t0) cc_final: 0.8398 (t0) REVERT: E 84 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8143 (mp0) REVERT: B 62 ASN cc_start: 0.8671 (m-40) cc_final: 0.8438 (t0) REVERT: B 221 MET cc_start: 0.7733 (mtp) cc_final: 0.7493 (mtp) REVERT: A 368 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7914 (mm-30) REVERT: A 369 MET cc_start: 0.8652 (mmm) cc_final: 0.8336 (mmm) REVERT: A 401 ASP cc_start: 0.8173 (t0) cc_final: 0.7786 (m-30) REVERT: A 470 GLU cc_start: 0.7773 (tt0) cc_final: 0.7515 (tt0) REVERT: A 545 MET cc_start: 0.8851 (mtp) cc_final: 0.8614 (mtm) REVERT: A 606 ASN cc_start: 0.8446 (m110) cc_final: 0.8213 (m110) REVERT: A 635 TRP cc_start: 0.8073 (m-90) cc_final: 0.7455 (m100) REVERT: A 651 ASN cc_start: 0.8731 (m-40) cc_final: 0.8294 (m-40) REVERT: A 743 THR cc_start: 0.8884 (t) cc_final: 0.8464 (m) REVERT: A 768 MET cc_start: 0.7422 (ttp) cc_final: 0.7012 (ttm) REVERT: A 776 TRP cc_start: 0.8810 (t60) cc_final: 0.7991 (t60) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.4824 time to fit residues: 186.3198 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 : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS A 186 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.163561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124724 restraints weight = 57607.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129754 restraints weight = 43013.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.130219 restraints weight = 29965.101| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10612 Z= 0.238 Angle : 0.584 5.046 14419 Z= 0.329 Chirality : 0.043 0.155 1563 Planarity : 0.004 0.049 1896 Dihedral : 4.818 22.093 1453 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1302 helix: 1.29 (0.30), residues: 272 sheet: 0.22 (0.24), residues: 421 loop : -0.43 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 576 HIS 0.006 0.001 HIS E 83 PHE 0.015 0.002 PHE A 648 TYR 0.021 0.002 TYR D 184 ARG 0.005 0.001 ARG D 197 Details of bonding type rmsd hydrogen bonds : bond 0.04796 ( 462) hydrogen bonds : angle 5.59706 ( 1263) SS BOND : bond 0.00736 ( 2) SS BOND : angle 0.98314 ( 4) covalent geometry : bond 0.00511 (10610) covalent geometry : angle 0.58342 (14415) *********************** 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 264 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.923 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: D 74 ASP cc_start: 0.9196 (m-30) cc_final: 0.8981 (m-30) REVERT: D 79 TYR cc_start: 0.8960 (m-80) cc_final: 0.8335 (m-10) REVERT: D 82 ASN cc_start: 0.8725 (t0) cc_final: 0.8407 (t0) REVERT: D 115 THR cc_start: 0.8965 (m) cc_final: 0.8728 (m) REVERT: D 136 ASP cc_start: 0.9098 (t0) cc_final: 0.8717 (t0) REVERT: D 187 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8372 (tm-30) REVERT: D 199 GLU cc_start: 0.8708 (tt0) cc_final: 0.8457 (tt0) REVERT: C 49 GLU cc_start: 0.8420 (mp0) cc_final: 0.8163 (mm-30) REVERT: C 64 ASP cc_start: 0.8968 (t0) cc_final: 0.8578 (t0) REVERT: E 84 GLU cc_start: 0.8594 (mm-30) cc_final: 0.7989 (mp0) REVERT: B 76 ASP cc_start: 0.6494 (t0) cc_final: 0.6241 (t0) REVERT: B 154 ARG cc_start: 0.8730 (ttp80) cc_final: 0.8450 (mtp-110) REVERT: B 165 HIS cc_start: 0.8136 (t-90) cc_final: 0.7935 (t-90) REVERT: B 221 MET cc_start: 0.7782 (mtp) cc_final: 0.7569 (mtp) REVERT: A 285 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7967 (tm-30) REVERT: A 303 LYS cc_start: 0.8590 (tmmt) cc_final: 0.8347 (tmtt) REVERT: A 304 MET cc_start: 0.8210 (tpp) cc_final: 0.7857 (tpp) REVERT: A 368 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8090 (mm-30) REVERT: A 470 GLU cc_start: 0.7895 (tt0) cc_final: 0.7671 (tt0) REVERT: A 606 ASN cc_start: 0.8429 (m110) cc_final: 0.8186 (m110) REVERT: A 651 ASN cc_start: 0.8816 (m-40) cc_final: 0.8517 (m110) REVERT: A 768 MET cc_start: 0.7414 (ttp) cc_final: 0.6992 (ttm) REVERT: A 776 TRP cc_start: 0.8900 (t60) cc_final: 0.8001 (t60) REVERT: A 789 GLN cc_start: 0.8091 (pt0) cc_final: 0.7708 (pt0) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.5425 time to fit residues: 198.4665 Evaluate side-chains 225 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 127 optimal weight: 0.0670 chunk 82 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.167356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128590 restraints weight = 57190.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132915 restraints weight = 41838.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133491 restraints weight = 31987.981| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10612 Z= 0.101 Angle : 0.500 4.505 14419 Z= 0.274 Chirality : 0.042 0.150 1563 Planarity : 0.004 0.058 1896 Dihedral : 4.585 30.304 1453 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.09 % Allowed : 0.45 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.23), residues: 1302 helix: 1.88 (0.31), residues: 273 sheet: 0.32 (0.25), residues: 405 loop : -0.29 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 48 HIS 0.003 0.001 HIS B 64 PHE 0.018 0.001 PHE A 648 TYR 0.026 0.001 TYR A 550 ARG 0.007 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 462) hydrogen bonds : angle 5.11618 ( 1263) SS BOND : bond 0.00264 ( 2) SS BOND : angle 2.51597 ( 4) covalent geometry : bond 0.00210 (10610) covalent geometry : angle 0.49786 (14415) *********************** 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 267 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 1.529 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: 0.8845 (m-80) cc_final: 0.8008 (m-10) REVERT: D 115 THR cc_start: 0.8921 (m) cc_final: 0.8695 (m) REVERT: D 136 ASP cc_start: 0.8913 (t0) cc_final: 0.8519 (t0) REVERT: D 187 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8187 (tm-30) REVERT: C 49 GLU cc_start: 0.8415 (mp0) cc_final: 0.8173 (mm-30) REVERT: C 56 MET cc_start: 0.8651 (tpp) cc_final: 0.7906 (tpp) REVERT: C 57 ILE cc_start: 0.9127 (tp) cc_final: 0.8795 (tp) REVERT: C 64 ASP cc_start: 0.8936 (t0) cc_final: 0.8442 (t0) REVERT: E 53 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8942 (mm-40) REVERT: E 84 GLU cc_start: 0.8589 (mm-30) cc_final: 0.7992 (mp0) REVERT: B 388 TYR cc_start: 0.6883 (m-80) cc_final: 0.6518 (m-80) REVERT: A 369 MET cc_start: 0.8639 (mmm) cc_final: 0.8395 (mmm) REVERT: A 470 GLU cc_start: 0.7850 (tt0) cc_final: 0.7617 (tt0) REVERT: A 606 ASN cc_start: 0.8472 (m110) cc_final: 0.8255 (m110) REVERT: A 609 TYR cc_start: 0.8288 (p90) cc_final: 0.7942 (p90) REVERT: A 651 ASN cc_start: 0.8669 (m-40) cc_final: 0.8328 (m110) REVERT: A 768 MET cc_start: 0.7370 (ttp) cc_final: 0.6926 (ttm) REVERT: A 776 TRP cc_start: 0.8864 (t60) cc_final: 0.7933 (t60) REVERT: A 789 GLN cc_start: 0.7997 (pt0) cc_final: 0.7781 (pt0) outliers start: 1 outliers final: 1 residues processed: 267 average time/residue: 0.5006 time to fit residues: 185.6360 Evaluate side-chains 235 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 4 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.0170 chunk 58 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.167566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.128939 restraints weight = 57385.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.136536 restraints weight = 38078.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136253 restraints weight = 22564.818| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10612 Z= 0.104 Angle : 0.486 4.253 14419 Z= 0.265 Chirality : 0.042 0.153 1563 Planarity : 0.003 0.040 1896 Dihedral : 4.462 29.939 1453 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1302 helix: 2.01 (0.31), residues: 274 sheet: 0.34 (0.25), residues: 404 loop : -0.24 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 739 HIS 0.004 0.001 HIS A 280 PHE 0.022 0.001 PHE A 648 TYR 0.020 0.001 TYR A 550 ARG 0.002 0.000 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 462) hydrogen bonds : angle 5.02411 ( 1263) SS BOND : bond 0.00258 ( 2) SS BOND : angle 1.97963 ( 4) covalent geometry : bond 0.00220 (10610) covalent geometry : angle 0.48497 (14415) *********************** 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 261 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 1.732 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: 0.8810 (m-80) cc_final: 0.8271 (m-10) REVERT: D 136 ASP cc_start: 0.8916 (t0) cc_final: 0.8425 (t0) REVERT: D 187 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8161 (tm-30) REVERT: C 49 GLU cc_start: 0.8299 (mp0) cc_final: 0.8067 (mm-30) REVERT: C 64 ASP cc_start: 0.8913 (t0) cc_final: 0.8408 (t0) REVERT: E 84 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8192 (mm-30) REVERT: B 163 LEU cc_start: 0.9208 (mt) cc_final: 0.8981 (mt) REVERT: B 388 TYR cc_start: 0.6824 (m-80) cc_final: 0.6461 (m-80) REVERT: A 470 GLU cc_start: 0.7859 (tt0) cc_final: 0.7615 (tt0) REVERT: A 606 ASN cc_start: 0.8490 (m110) cc_final: 0.8285 (m110) REVERT: A 651 ASN cc_start: 0.8693 (m-40) cc_final: 0.8304 (m110) REVERT: A 711 MET cc_start: 0.8577 (ptt) cc_final: 0.8351 (ptt) REVERT: A 768 MET cc_start: 0.7302 (ttp) cc_final: 0.6872 (ttm) REVERT: A 776 TRP cc_start: 0.8817 (t60) cc_final: 0.7897 (t60) outliers start: 1 outliers final: 1 residues processed: 261 average time/residue: 0.5246 time to fit residues: 190.0093 Evaluate side-chains 234 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 HIS ** 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 = 0.4033 r_free = 0.4033 target = 0.167324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.128911 restraints weight = 54618.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.136402 restraints weight = 36982.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.135564 restraints weight = 25410.657| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10612 Z= 0.168 Angle : 0.516 4.185 14419 Z= 0.286 Chirality : 0.042 0.149 1563 Planarity : 0.004 0.051 1896 Dihedral : 4.573 30.088 1453 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.23), residues: 1302 helix: 1.86 (0.30), residues: 272 sheet: 0.25 (0.25), residues: 409 loop : -0.45 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 546 HIS 0.004 0.001 HIS E 83 PHE 0.018 0.001 PHE A 648 TYR 0.023 0.002 TYR A 550 ARG 0.003 0.001 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 462) hydrogen bonds : angle 5.20482 ( 1263) SS BOND : bond 0.00374 ( 2) SS BOND : angle 1.82559 ( 4) covalent geometry : bond 0.00367 (10610) covalent geometry : angle 0.51481 (14415) *********************** 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 259 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.545 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: D 79 TYR cc_start: 0.8811 (m-80) cc_final: 0.8256 (m-10) REVERT: D 115 THR cc_start: 0.8930 (m) cc_final: 0.8708 (m) REVERT: D 136 ASP cc_start: 0.9018 (t0) cc_final: 0.8621 (t0) REVERT: D 187 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8207 (tm-30) REVERT: C 49 GLU cc_start: 0.8328 (mp0) cc_final: 0.8077 (mm-30) REVERT: C 64 ASP cc_start: 0.8990 (t0) cc_final: 0.8493 (t0) REVERT: E 84 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8244 (mm-30) REVERT: B 82 LYS cc_start: 0.7950 (mttp) cc_final: 0.7538 (mmtt) REVERT: B 165 HIS cc_start: 0.8019 (t-90) cc_final: 0.7732 (t-90) REVERT: A 285 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7979 (tm-30) REVERT: A 369 MET cc_start: 0.8436 (mmm) cc_final: 0.8125 (mmm) REVERT: A 394 PHE cc_start: 0.9539 (m-10) cc_final: 0.9223 (m-10) REVERT: A 470 GLU cc_start: 0.7853 (tt0) cc_final: 0.7639 (tt0) REVERT: A 606 ASN cc_start: 0.8433 (m110) cc_final: 0.8179 (m110) REVERT: A 651 ASN cc_start: 0.8787 (m-40) cc_final: 0.8404 (m110) REVERT: A 711 MET cc_start: 0.8651 (ptt) cc_final: 0.8437 (ptt) REVERT: A 768 MET cc_start: 0.7315 (ttp) cc_final: 0.6902 (ttm) REVERT: A 776 TRP cc_start: 0.8843 (t60) cc_final: 0.7834 (t60) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.5173 time to fit residues: 187.9253 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 : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 32 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 0.0070 chunk 46 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 0.0270 chunk 12 optimal weight: 0.0980 chunk 75 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.167013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123828 restraints weight = 54286.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.125902 restraints weight = 25729.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127689 restraints weight = 19045.775| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.6060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10612 Z= 0.092 Angle : 0.485 4.861 14419 Z= 0.262 Chirality : 0.042 0.153 1563 Planarity : 0.004 0.045 1896 Dihedral : 4.409 35.548 1453 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1302 helix: 2.20 (0.31), residues: 274 sheet: 0.32 (0.25), residues: 404 loop : -0.37 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 279 HIS 0.003 0.001 HIS A 533 PHE 0.016 0.001 PHE A 648 TYR 0.021 0.001 TYR A 550 ARG 0.003 0.000 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 462) hydrogen bonds : angle 4.86834 ( 1263) SS BOND : bond 0.00235 ( 2) SS BOND : angle 1.56388 ( 4) covalent geometry : bond 0.00199 (10610) covalent geometry : angle 0.48461 (14415) ********************** 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 : 1.526 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: 0.8744 (m-80) cc_final: 0.8224 (m-10) REVERT: D 115 THR cc_start: 0.8836 (m) cc_final: 0.8616 (m) REVERT: D 136 ASP cc_start: 0.8909 (t0) cc_final: 0.8481 (t0) REVERT: D 187 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8082 (tm-30) REVERT: C 49 GLU cc_start: 0.8313 (mp0) cc_final: 0.8053 (mm-30) REVERT: C 56 MET cc_start: 0.8686 (tpp) cc_final: 0.7731 (tpp) REVERT: C 57 ILE cc_start: 0.9167 (tp) cc_final: 0.8777 (tp) REVERT: C 64 ASP cc_start: 0.8839 (t0) cc_final: 0.8302 (t0) REVERT: E 84 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8177 (mm-30) REVERT: B 388 TYR cc_start: 0.6838 (m-80) cc_final: 0.6459 (m-80) REVERT: A 394 PHE cc_start: 0.9500 (m-10) cc_final: 0.9138 (m-10) REVERT: A 470 GLU cc_start: 0.7878 (tt0) cc_final: 0.7624 (tt0) REVERT: A 606 ASN cc_start: 0.8459 (m110) cc_final: 0.8243 (m110) REVERT: A 609 TYR cc_start: 0.8331 (p90) cc_final: 0.8121 (p90) REVERT: A 768 MET cc_start: 0.7197 (ttp) cc_final: 0.6703 (ttm) REVERT: A 776 TRP cc_start: 0.8700 (t60) cc_final: 0.7690 (t60) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.4962 time to fit residues: 177.6901 Evaluate side-chains 235 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 61 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.165156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126236 restraints weight = 55084.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132065 restraints weight = 37972.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131742 restraints weight = 29025.562| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.6226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10612 Z= 0.196 Angle : 0.533 4.876 14419 Z= 0.295 Chirality : 0.043 0.195 1563 Planarity : 0.004 0.070 1896 Dihedral : 4.539 34.192 1453 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.23), residues: 1302 helix: 1.72 (0.30), residues: 272 sheet: 0.24 (0.25), residues: 406 loop : -0.57 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 576 HIS 0.010 0.001 HIS A 533 PHE 0.018 0.001 PHE A 648 TYR 0.020 0.002 TYR A 550 ARG 0.004 0.001 ARG D 197 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 462) hydrogen bonds : angle 5.22140 ( 1263) SS BOND : bond 0.00384 ( 2) SS BOND : angle 1.66513 ( 4) covalent geometry : bond 0.00429 (10610) covalent geometry : angle 0.53216 (14415) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6755.05 seconds wall clock time: 115 minutes 58.26 seconds (6958.26 seconds total)