Starting phenix.real_space_refine on Thu Jul 31 08:50:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qn4_18507/07_2025/8qn4_18507.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qn4_18507/07_2025/8qn4_18507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qn4_18507/07_2025/8qn4_18507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qn4_18507/07_2025/8qn4_18507.map" model { file = "/net/cci-nas-00/data/ceres_data/8qn4_18507/07_2025/8qn4_18507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qn4_18507/07_2025/8qn4_18507.cif" } resolution = 3.36 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= -0.000 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 8571 2.51 5 N 2324 2.21 5 O 2674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13608 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6231 Classifications: {'peptide': 787} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 757} Chain: "B" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2750 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 355} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 407 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 5, 'TRANS': 50} Chain: "D" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1722 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 645 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "F" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1853 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 233} Chain breaks: 5 Time building chain proxies: 7.61, per 1000 atoms: 0.56 Number of scatterers: 13608 At special positions: 0 Unit cell: (126.48, 123.69, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 2674 8.00 N 2324 7.00 C 8571 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS F1293 " distance=2.04 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: 2.83 Conformation dependent library (CDL) restraints added in 1.7 seconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3172 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 16 sheets defined 19.7% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.829A pdb=" N ILE A 59 " --> pdb=" O ASN A 55 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.686A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN A 113 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 144 removed outlier: 4.043A pdb=" N ASP A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.529A pdb=" N GLY A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.727A pdb=" N VAL A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.293A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 removed outlier: 3.716A pdb=" N ARG A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.502A pdb=" N MET A 552 " --> pdb=" O TYR A 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.547A pdb=" N LEU C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 removed outlier: 3.521A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 62 removed outlier: 3.780A pdb=" N ALA D 57 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 83 removed outlier: 3.587A pdb=" N TYR D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 removed outlier: 3.542A pdb=" N ALA D 90 " --> pdb=" O PRO D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.503A pdb=" N MET D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR D 110 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY D 113 " --> pdb=" O MET D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 154 Processing helix chain 'D' and resid 158 through 186 removed outlier: 4.667A pdb=" N ASP D 162 " --> pdb=" O GLN D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.693A pdb=" N VAL D 195 " --> pdb=" O TRP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.594A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.630A pdb=" N MET D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 240 Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.691A pdb=" N TYR E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 1012 through 1034 removed outlier: 4.122A pdb=" N ASN F1026 " --> pdb=" O VAL F1022 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG F1028 " --> pdb=" O ASN F1024 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N MET F1029 " --> pdb=" O LEU F1025 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 3.558A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.948A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N SER A 100 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 177 through 183 removed outlier: 7.355A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 255 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 removed outlier: 3.957A pdb=" N GLU A 294 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLY A 270 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.718A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP A 399 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 802 through 806 removed outlier: 4.228A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP A 745 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 487 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N TYR A 454 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 448 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA F1266 " --> pdb=" O PHE F1274 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F1282 " --> pdb=" O MET F1258 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU F1202 " --> pdb=" O LEU F1233 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE F1203 " --> pdb=" O VAL F1174 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA F1117 " --> pdb=" O PHE F1113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 673 removed outlier: 6.615A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 50 through 51 removed outlier: 4.041A pdb=" N THR B 50 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 removed outlier: 4.140A pdb=" N ALA B 74 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 202 Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.863A pdb=" N ARG B 281 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 269 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.536A pdb=" N ILE B 290 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP B 292 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.512A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.615A pdb=" N THR E 94 " --> pdb=" O ASN E 103 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1740 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.61 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2922 1.34 - 1.46: 4941 1.46 - 1.59: 5965 1.59 - 1.72: 0 1.72 - 1.84: 74 Bond restraints: 13902 Sorted by residual: bond pdb=" CA VAL B 286 " pdb=" C VAL B 286 " ideal model delta sigma weight residual 1.524 1.465 0.060 1.06e-02 8.90e+03 3.17e+01 bond pdb=" CA GLY B 210 " pdb=" C GLY B 210 " ideal model delta sigma weight residual 1.517 1.467 0.050 9.60e-03 1.09e+04 2.72e+01 bond pdb=" CA TYR D 62 " pdb=" CB TYR D 62 " ideal model delta sigma weight residual 1.527 1.576 -0.049 1.05e-02 9.07e+03 2.18e+01 bond pdb=" CA GLY F1211 " pdb=" C GLY F1211 " ideal model delta sigma weight residual 1.513 1.467 0.046 1.08e-02 8.57e+03 1.79e+01 bond pdb=" CA SER A 657 " pdb=" C SER A 657 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.28e-02 6.10e+03 1.74e+01 ... (remaining 13897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 17285 3.61 - 7.21: 1497 7.21 - 10.82: 82 10.82 - 14.42: 5 14.42 - 18.03: 2 Bond angle restraints: 18871 Sorted by residual: angle pdb=" N GLY B 196 " pdb=" CA GLY B 196 " pdb=" C GLY B 196 " ideal model delta sigma weight residual 112.04 94.01 18.03 1.02e+00 9.61e-01 3.12e+02 angle pdb=" C VAL B 286 " pdb=" CA VAL B 286 " pdb=" CB VAL B 286 " ideal model delta sigma weight residual 111.05 102.79 8.26 8.90e-01 1.26e+00 8.61e+01 angle pdb=" CA ASP A 493 " pdb=" CB ASP A 493 " pdb=" CG ASP A 493 " ideal model delta sigma weight residual 112.60 121.22 -8.62 1.00e+00 1.00e+00 7.43e+01 angle pdb=" CA ASN B 287 " pdb=" CB ASN B 287 " pdb=" CG ASN B 287 " ideal model delta sigma weight residual 112.60 104.15 8.45 1.00e+00 1.00e+00 7.14e+01 angle pdb=" N SER D 242 " pdb=" CA SER D 242 " pdb=" C SER D 242 " ideal model delta sigma weight residual 110.80 128.19 -17.39 2.13e+00 2.20e-01 6.66e+01 ... (remaining 18866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.76: 7655 18.76 - 37.51: 367 37.51 - 56.27: 77 56.27 - 75.02: 54 75.02 - 93.78: 28 Dihedral angle restraints: 8181 sinusoidal: 3186 harmonic: 4995 Sorted by residual: dihedral pdb=" CA LYS B 280 " pdb=" C LYS B 280 " pdb=" N ARG B 281 " pdb=" CA ARG B 281 " ideal model delta harmonic sigma weight residual 180.00 135.24 44.76 0 5.00e+00 4.00e-02 8.01e+01 dihedral pdb=" N SER D 243 " pdb=" C SER D 243 " pdb=" CA SER D 243 " pdb=" CB SER D 243 " ideal model delta harmonic sigma weight residual 122.80 140.97 -18.17 0 2.50e+00 1.60e-01 5.28e+01 dihedral pdb=" N SER D 242 " pdb=" C SER D 242 " pdb=" CA SER D 242 " pdb=" CB SER D 242 " ideal model delta harmonic sigma weight residual 122.80 139.91 -17.11 0 2.50e+00 1.60e-01 4.68e+01 ... (remaining 8178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 1705 0.158 - 0.317: 308 0.317 - 0.475: 25 0.475 - 0.634: 4 0.634 - 0.792: 1 Chirality restraints: 2043 Sorted by residual: chirality pdb=" CA SER D 242 " pdb=" N SER D 242 " pdb=" C SER D 242 " pdb=" CB SER D 242 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" CA ARG F1269 " pdb=" N ARG F1269 " pdb=" C ARG F1269 " pdb=" CB ARG F1269 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" CA SER D 243 " pdb=" N SER D 243 " pdb=" C SER D 243 " pdb=" CB SER D 243 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.02e+00 ... (remaining 2040 not shown) Planarity restraints: 2482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 686 " 0.151 2.00e-02 2.50e+03 1.22e-01 2.99e+02 pdb=" CG TYR A 686 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 686 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR A 686 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 TYR A 686 " -0.155 2.00e-02 2.50e+03 pdb=" CE2 TYR A 686 " -0.093 2.00e-02 2.50e+03 pdb=" CZ TYR A 686 " -0.045 2.00e-02 2.50e+03 pdb=" OH TYR A 686 " 0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 255 " -0.216 2.00e-02 2.50e+03 1.12e-01 2.53e+02 pdb=" CG TYR A 255 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR A 255 " 0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR A 255 " 0.124 2.00e-02 2.50e+03 pdb=" CE1 TYR A 255 " 0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR A 255 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 255 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 255 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F1274 " -0.132 2.00e-02 2.50e+03 1.02e-01 1.83e+02 pdb=" CG PHE F1274 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE F1274 " 0.183 2.00e-02 2.50e+03 pdb=" CD2 PHE F1274 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE F1274 " -0.084 2.00e-02 2.50e+03 pdb=" CE2 PHE F1274 " 0.043 2.00e-02 2.50e+03 pdb=" CZ PHE F1274 " -0.097 2.00e-02 2.50e+03 ... (remaining 2479 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1240 2.75 - 3.29: 12249 3.29 - 3.82: 21911 3.82 - 4.36: 27852 4.36 - 4.90: 46384 Nonbonded interactions: 109636 Sorted by model distance: nonbonded pdb=" N GLY B 196 " pdb=" O GLY B 196 " model vdw 2.210 2.496 nonbonded pdb=" N THR F1162 " pdb=" O THR F1162 " model vdw 2.405 2.496 nonbonded pdb=" N TYR A 432 " pdb=" O TYR A 432 " model vdw 2.438 2.496 nonbonded pdb=" N SER B 126 " pdb=" O SER B 126 " model vdw 2.453 2.496 nonbonded pdb=" N GLY A 638 " pdb=" O GLY A 638 " model vdw 2.461 2.496 ... (remaining 109631 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.410 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4438 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 : 0.017 0.061 13904 Z= 1.033 Angle : 2.082 18.029 18875 Z= 1.402 Chirality : 0.121 0.792 2043 Planarity : 0.019 0.220 2482 Dihedral : 14.779 93.777 5003 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.64 % Favored : 94.24 % Rotamer: Outliers : 0.76 % Allowed : 5.53 % Favored : 93.71 % Cbeta Deviations : 0.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.18), residues: 1720 helix: -0.33 (0.28), residues: 316 sheet: -0.36 (0.21), residues: 548 loop : -2.43 (0.17), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.167 0.024 TRP B 183 HIS 0.025 0.006 HIS B 324 PHE 0.183 0.020 PHE F1274 TYR 0.230 0.030 TYR A 686 ARG 0.057 0.004 ARG F1224 Details of bonding type rmsd hydrogen bonds : bond 0.25438 ( 620) hydrogen bonds : angle 9.60040 ( 1740) SS BOND : bond 0.00437 ( 2) SS BOND : angle 6.69989 ( 4) covalent geometry : bond 0.01672 (13902) covalent geometry : angle 2.07952 (18871) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 504 time to evaluate : 1.438 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: A 166 LYS cc_start: 0.1622 (OUTLIER) cc_final: 0.0035 (ptmm) REVERT: A 177 ILE cc_start: 0.5462 (mm) cc_final: 0.5155 (mm) REVERT: A 182 ILE cc_start: 0.7992 (mm) cc_final: 0.7774 (mm) REVERT: A 361 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6984 (pttt) REVERT: F 1218 ASP cc_start: 0.4117 (p0) cc_final: 0.3623 (p0) outliers start: 11 outliers final: 3 residues processed: 513 average time/residue: 0.3087 time to fit residues: 220.3002 Evaluate side-chains 289 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 284 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 155 optimal weight: 30.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 102 ASN A 170 GLN A 215 GLN ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN A 411 GLN A 563 ASN A 748 ASN A 803 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 350 ASN D 54 GLN D 60 ASN ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 54 GLN E 71 ASN F1023 ASN F1024 ASN F1064 GLN ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.249603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.207887 restraints weight = 17137.629| |-----------------------------------------------------------------------------| r_work (start): 0.4581 rms_B_bonded: 2.95 r_work: 0.4388 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 13904 Z= 0.181 Angle : 0.698 9.190 18875 Z= 0.376 Chirality : 0.048 0.161 2043 Planarity : 0.005 0.041 2482 Dihedral : 6.168 76.185 1921 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.50 % Allowed : 11.96 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.34 (0.18), residues: 1720 helix: 0.44 (0.27), residues: 328 sheet: -0.21 (0.20), residues: 580 loop : -1.99 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 93 HIS 0.013 0.002 HIS D 102 PHE 0.031 0.002 PHE A 565 TYR 0.038 0.002 TYR D 79 ARG 0.009 0.001 ARG B 273 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 620) hydrogen bonds : angle 6.36366 ( 1740) SS BOND : bond 0.00011 ( 2) SS BOND : angle 2.06715 ( 4) covalent geometry : bond 0.00374 (13902) covalent geometry : angle 0.69697 (18871) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 301 time to evaluate : 1.627 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: A 181 ASN cc_start: 0.7655 (m110) cc_final: 0.6882 (m110) REVERT: A 244 GLN cc_start: 0.7626 (mm-40) cc_final: 0.7325 (mp10) REVERT: A 294 GLU cc_start: 0.6233 (mp0) cc_final: 0.5999 (mp0) REVERT: B 127 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7659 (mt-10) REVERT: B 304 ARG cc_start: 0.6936 (mtp180) cc_final: 0.6489 (ttp-110) REVERT: B 310 ILE cc_start: 0.6136 (OUTLIER) cc_final: 0.5922 (mt) REVERT: D 35 ILE cc_start: 0.6699 (mm) cc_final: 0.6486 (mm) REVERT: D 232 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7484 (pp20) REVERT: F 1023 ASN cc_start: 0.8688 (m-40) cc_final: 0.8433 (m-40) REVERT: F 1168 GLU cc_start: 0.4187 (mp0) cc_final: 0.3826 (mp0) REVERT: F 1212 LYS cc_start: 0.6089 (OUTLIER) cc_final: 0.5723 (ttpp) outliers start: 65 outliers final: 33 residues processed: 341 average time/residue: 0.3708 time to fit residues: 181.2380 Evaluate side-chains 279 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1212 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 41 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 136 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 0.0070 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN A 533 HIS ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 336 ASN B 350 ASN B 368 GLN D 138 GLN E 53 GLN E 54 GLN ** F1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1130 ASN F1160 HIS ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1271 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.239591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.186504 restraints weight = 17132.989| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 3.41 r_work: 0.4192 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13904 Z= 0.156 Angle : 0.637 8.878 18875 Z= 0.340 Chirality : 0.045 0.163 2043 Planarity : 0.004 0.037 2482 Dihedral : 5.607 76.136 1912 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.08 % Allowed : 16.39 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.19), residues: 1720 helix: 0.92 (0.28), residues: 331 sheet: -0.19 (0.20), residues: 577 loop : -1.68 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 546 HIS 0.010 0.001 HIS D 102 PHE 0.026 0.002 PHE D 95 TYR 0.038 0.002 TYR D 79 ARG 0.006 0.001 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 620) hydrogen bonds : angle 5.67446 ( 1740) SS BOND : bond 0.00322 ( 2) SS BOND : angle 2.42290 ( 4) covalent geometry : bond 0.00332 (13902) covalent geometry : angle 0.63609 (18871) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 256 time to evaluate : 1.585 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: A 181 ASN cc_start: 0.7648 (m110) cc_final: 0.6928 (m110) REVERT: A 259 ASN cc_start: 0.8483 (m110) cc_final: 0.8228 (m-40) REVERT: A 797 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.6422 (t0) REVERT: A 805 ASN cc_start: 0.8484 (t0) cc_final: 0.8164 (t0) REVERT: B 163 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8034 (mt) REVERT: B 384 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7510 (p0) REVERT: D 232 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7485 (pp20) REVERT: F 1212 LYS cc_start: 0.6085 (OUTLIER) cc_final: 0.5620 (ttpp) REVERT: F 1259 LEU cc_start: 0.6685 (mm) cc_final: 0.6257 (tt) outliers start: 59 outliers final: 43 residues processed: 293 average time/residue: 0.2693 time to fit residues: 115.1669 Evaluate side-chains 270 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 222 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 1085 THR Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1128 HIS Chi-restraints excluded: chain F residue 1130 ASN Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1212 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN A 803 GLN B 85 ASN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN E 80 GLN E 89 GLN ** F1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1230 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.229495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.167173 restraints weight = 16771.948| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 3.48 r_work: 0.4005 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.6851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 13904 Z= 0.245 Angle : 0.700 10.950 18875 Z= 0.372 Chirality : 0.047 0.173 2043 Planarity : 0.005 0.060 2482 Dihedral : 5.744 79.732 1911 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.46 % Allowed : 16.11 % Favored : 78.42 % 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: -1.04 (0.19), residues: 1720 helix: 0.72 (0.28), residues: 335 sheet: -0.20 (0.20), residues: 599 loop : -1.71 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 739 HIS 0.008 0.001 HIS D 102 PHE 0.025 0.002 PHE D 95 TYR 0.036 0.002 TYR D 79 ARG 0.009 0.001 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 620) hydrogen bonds : angle 5.67693 ( 1740) SS BOND : bond 0.00663 ( 2) SS BOND : angle 2.83762 ( 4) covalent geometry : bond 0.00542 (13902) covalent geometry : angle 0.69912 (18871) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 254 time to evaluate : 1.583 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: A 197 PHE cc_start: 0.7490 (m-80) cc_final: 0.7098 (m-80) REVERT: A 432 TYR cc_start: 0.6158 (t80) cc_final: 0.5956 (m-80) REVERT: A 545 MET cc_start: 0.7602 (mpp) cc_final: 0.7392 (mpp) REVERT: A 641 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7130 (mm) REVERT: A 737 PHE cc_start: 0.6883 (t80) cc_final: 0.6652 (t80) REVERT: A 797 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.6918 (t0) REVERT: A 805 ASN cc_start: 0.8730 (t0) cc_final: 0.8358 (t0) REVERT: B 163 LEU cc_start: 0.8382 (mp) cc_final: 0.8164 (mt) REVERT: B 197 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6253 (mt-10) REVERT: B 384 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7539 (p0) REVERT: D 188 ARG cc_start: 0.6724 (mmt-90) cc_final: 0.6076 (tpm170) REVERT: D 232 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7342 (pp20) REVERT: F 1154 GLU cc_start: 0.6669 (tt0) cc_final: 0.6247 (tm-30) REVERT: F 1212 LYS cc_start: 0.5738 (OUTLIER) cc_final: 0.5330 (ttpp) REVERT: F 1217 LYS cc_start: 0.5402 (OUTLIER) cc_final: 0.3968 (mtmm) REVERT: F 1259 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.5915 (tt) REVERT: F 1274 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.6130 (m-10) outliers start: 79 outliers final: 53 residues processed: 295 average time/residue: 0.2678 time to fit residues: 114.4733 Evaluate side-chains 295 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 233 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1085 THR Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1128 HIS Chi-restraints excluded: chain F residue 1172 GLU Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1212 LYS Chi-restraints excluded: chain F residue 1217 LYS Chi-restraints excluded: chain F residue 1259 LEU Chi-restraints excluded: chain F residue 1274 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 93 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 17 optimal weight: 0.2980 chunk 102 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN E 36 ASN E 52 GLN E 54 GLN ** F1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1160 HIS ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.231268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.170577 restraints weight = 16970.540| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 3.39 r_work: 0.4051 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.7231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13904 Z= 0.148 Angle : 0.609 9.400 18875 Z= 0.321 Chirality : 0.045 0.146 2043 Planarity : 0.004 0.033 2482 Dihedral : 5.238 68.136 1909 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.36 % Allowed : 18.05 % Favored : 77.59 % 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: -0.83 (0.19), residues: 1720 helix: 1.10 (0.28), residues: 331 sheet: -0.15 (0.20), residues: 596 loop : -1.58 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 183 HIS 0.014 0.001 HIS D 102 PHE 0.029 0.002 PHE D 95 TYR 0.026 0.001 TYR D 79 ARG 0.006 0.001 ARG D 212 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 620) hydrogen bonds : angle 5.33705 ( 1740) SS BOND : bond 0.00441 ( 2) SS BOND : angle 2.30063 ( 4) covalent geometry : bond 0.00325 (13902) covalent geometry : angle 0.60862 (18871) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 242 time to evaluate : 1.422 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: A 737 PHE cc_start: 0.6742 (t80) cc_final: 0.6517 (t80) REVERT: A 745 TRP cc_start: 0.7425 (p-90) cc_final: 0.7070 (p90) REVERT: A 797 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.6319 (t0) REVERT: A 805 ASN cc_start: 0.8891 (t0) cc_final: 0.8587 (t0) REVERT: B 163 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8042 (mt) REVERT: B 341 ASP cc_start: 0.5331 (p0) cc_final: 0.5113 (p0) REVERT: D 188 ARG cc_start: 0.6606 (mmt-90) cc_final: 0.6046 (tpm170) REVERT: D 232 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7357 (pp20) REVERT: E 54 GLN cc_start: 0.8142 (pt0) cc_final: 0.7904 (pt0) REVERT: F 1212 LYS cc_start: 0.5780 (OUTLIER) cc_final: 0.5370 (ttpt) REVERT: F 1259 LEU cc_start: 0.6304 (mm) cc_final: 0.5819 (tt) outliers start: 63 outliers final: 46 residues processed: 279 average time/residue: 0.2680 time to fit residues: 108.8357 Evaluate side-chains 269 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 550 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1128 HIS Chi-restraints excluded: chain F residue 1172 GLU Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1212 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 134 optimal weight: 0.2980 chunk 150 optimal weight: 8.9990 chunk 99 optimal weight: 0.0370 chunk 45 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 92 optimal weight: 0.0000 chunk 73 optimal weight: 2.9990 overall best weight: 0.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN E 52 GLN F1026 ASN ** F1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.235615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.180038 restraints weight = 16940.204| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 3.48 r_work: 0.4095 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.7406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13904 Z= 0.103 Angle : 0.577 8.536 18875 Z= 0.301 Chirality : 0.043 0.151 2043 Planarity : 0.004 0.032 2482 Dihedral : 4.841 65.301 1909 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.80 % Allowed : 19.78 % Favored : 76.42 % 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 (0.20), residues: 1720 helix: 1.46 (0.29), residues: 338 sheet: 0.02 (0.21), residues: 579 loop : -1.48 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 749 HIS 0.008 0.001 HIS D 102 PHE 0.022 0.001 PHE D 95 TYR 0.033 0.001 TYR D 79 ARG 0.007 0.000 ARG D 212 Details of bonding type rmsd hydrogen bonds : bond 0.02967 ( 620) hydrogen bonds : angle 4.92849 ( 1740) SS BOND : bond 0.00284 ( 2) SS BOND : angle 1.93521 ( 4) covalent geometry : bond 0.00218 (13902) covalent geometry : angle 0.57605 (18871) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 254 time to evaluate : 1.457 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: A 550 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.7142 (m-80) REVERT: A 556 PRO cc_start: 0.5287 (Cg_exo) cc_final: 0.5077 (Cg_endo) REVERT: A 737 PHE cc_start: 0.6731 (t80) cc_final: 0.6508 (t80) REVERT: A 797 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.6288 (t0) REVERT: A 805 ASN cc_start: 0.8845 (t0) cc_final: 0.8555 (t0) REVERT: B 163 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7807 (mt) REVERT: D 188 ARG cc_start: 0.6499 (mmt-90) cc_final: 0.6073 (tpm170) REVERT: D 232 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7440 (pp20) REVERT: F 1129 ASP cc_start: 0.7697 (t70) cc_final: 0.7055 (p0) REVERT: F 1154 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6663 (tp30) REVERT: F 1212 LYS cc_start: 0.6037 (OUTLIER) cc_final: 0.5701 (ttpt) REVERT: F 1258 MET cc_start: 0.3861 (mmp) cc_final: 0.3642 (mmp) REVERT: F 1259 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.5867 (tt) outliers start: 55 outliers final: 38 residues processed: 288 average time/residue: 0.3050 time to fit residues: 128.2530 Evaluate side-chains 270 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 550 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1128 HIS Chi-restraints excluded: chain F residue 1154 GLU Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1212 LYS Chi-restraints excluded: chain F residue 1259 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 157 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A 448 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN B 130 GLN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN E 53 GLN F1024 ASN ** F1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1160 HIS ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.223536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.163009 restraints weight = 17053.810| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 3.41 r_work: 0.3932 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.8147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 13904 Z= 0.287 Angle : 0.738 8.967 18875 Z= 0.391 Chirality : 0.049 0.190 2043 Planarity : 0.005 0.053 2482 Dihedral : 5.513 62.743 1909 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.46 % Allowed : 19.57 % Favored : 74.97 % 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: -1.10 (0.19), residues: 1720 helix: 0.75 (0.28), residues: 339 sheet: -0.30 (0.21), residues: 572 loop : -1.70 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 183 HIS 0.013 0.002 HIS D 102 PHE 0.023 0.002 PHE E 77 TYR 0.041 0.002 TYR D 79 ARG 0.007 0.001 ARG E 47 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 620) hydrogen bonds : angle 5.56476 ( 1740) SS BOND : bond 0.00944 ( 2) SS BOND : angle 3.18230 ( 4) covalent geometry : bond 0.00642 (13902) covalent geometry : angle 0.73655 (18871) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 230 time to evaluate : 1.938 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: A 152 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6275 (mptm) REVERT: A 368 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7841 (mm-30) REVERT: A 459 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7622 (p0) REVERT: A 477 TYR cc_start: 0.8383 (m-80) cc_final: 0.8139 (m-80) REVERT: A 745 TRP cc_start: 0.7564 (p-90) cc_final: 0.7217 (p90) REVERT: A 805 ASN cc_start: 0.9011 (t0) cc_final: 0.8740 (t0) REVERT: B 32 MET cc_start: 0.6786 (mmm) cc_final: 0.6332 (mpp) REVERT: B 163 LEU cc_start: 0.8389 (mp) cc_final: 0.8079 (mt) REVERT: B 306 MET cc_start: 0.6014 (mtt) cc_final: 0.5593 (mtt) REVERT: D 184 TYR cc_start: 0.5818 (m-10) cc_final: 0.5596 (m-10) REVERT: D 188 ARG cc_start: 0.7258 (mmt-90) cc_final: 0.6246 (tpm170) REVERT: D 232 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7268 (pp20) REVERT: F 1154 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6719 (tp30) REVERT: F 1175 TYR cc_start: 0.4481 (t80) cc_final: 0.3369 (t80) REVERT: F 1212 LYS cc_start: 0.6097 (OUTLIER) cc_final: 0.5648 (ttpt) REVERT: F 1217 LYS cc_start: 0.5948 (OUTLIER) cc_final: 0.4222 (mtmm) REVERT: F 1224 ARG cc_start: 0.8160 (ptp90) cc_final: 0.7854 (ptp90) REVERT: F 1269 ARG cc_start: 0.8185 (mpp80) cc_final: 0.7960 (mpt-90) outliers start: 79 outliers final: 54 residues processed: 280 average time/residue: 0.3181 time to fit residues: 132.5851 Evaluate side-chains 282 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 459 ASN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1080 THR Chi-restraints excluded: chain F residue 1085 THR Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1154 GLU Chi-restraints excluded: chain F residue 1172 GLU Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1212 LYS Chi-restraints excluded: chain F residue 1217 LYS Chi-restraints excluded: chain F residue 1259 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 33 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 9 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 122 optimal weight: 0.0070 chunk 123 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS B 319 GLN B 368 GLN ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN F1026 ASN ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.229511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.173448 restraints weight = 16839.965| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 3.50 r_work: 0.3995 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.8218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13904 Z= 0.126 Angle : 0.633 17.598 18875 Z= 0.323 Chirality : 0.045 0.177 2043 Planarity : 0.004 0.047 2482 Dihedral : 5.016 57.777 1909 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.15 % Allowed : 21.51 % Favored : 74.34 % 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: -0.77 (0.20), residues: 1720 helix: 1.34 (0.29), residues: 327 sheet: -0.25 (0.21), residues: 584 loop : -1.50 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 739 HIS 0.009 0.001 HIS D 102 PHE 0.025 0.002 PHE A 440 TYR 0.041 0.001 TYR D 79 ARG 0.004 0.000 ARG D 212 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 620) hydrogen bonds : angle 5.16849 ( 1740) SS BOND : bond 0.00518 ( 2) SS BOND : angle 2.44437 ( 4) covalent geometry : bond 0.00275 (13902) covalent geometry : angle 0.63169 (18871) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 237 time to evaluate : 1.389 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: A 152 LYS cc_start: 0.6867 (OUTLIER) cc_final: 0.6284 (mptm) REVERT: A 368 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 459 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7393 (p0) REVERT: A 737 PHE cc_start: 0.6860 (t80) cc_final: 0.6586 (t80) REVERT: A 741 MET cc_start: 0.7676 (ptp) cc_final: 0.6945 (ptm) REVERT: A 745 TRP cc_start: 0.7526 (p-90) cc_final: 0.7257 (p90) REVERT: A 805 ASN cc_start: 0.9029 (t0) cc_final: 0.8774 (t0) REVERT: B 32 MET cc_start: 0.6864 (mmm) cc_final: 0.6376 (mpp) REVERT: B 163 LEU cc_start: 0.8282 (mp) cc_final: 0.7950 (mt) REVERT: B 221 MET cc_start: 0.6916 (tpp) cc_final: 0.6702 (mmm) REVERT: B 306 MET cc_start: 0.5822 (mtt) cc_final: 0.5487 (mtt) REVERT: B 341 ASP cc_start: 0.5431 (p0) cc_final: 0.4437 (p0) REVERT: C 56 MET cc_start: 0.7446 (ptp) cc_final: 0.7128 (ptp) REVERT: D 188 ARG cc_start: 0.6857 (mmt-90) cc_final: 0.6166 (tpm170) REVERT: D 232 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7399 (pp20) REVERT: F 1154 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6805 (tp30) REVERT: F 1175 TYR cc_start: 0.4403 (t80) cc_final: 0.3740 (t80) REVERT: F 1224 ARG cc_start: 0.8040 (ptp90) cc_final: 0.7746 (ptp90) REVERT: F 1258 MET cc_start: 0.3851 (mmp) cc_final: 0.3579 (mmp) REVERT: F 1259 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.5772 (tt) outliers start: 60 outliers final: 47 residues processed: 272 average time/residue: 0.2456 time to fit residues: 98.6262 Evaluate side-chains 277 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 225 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 459 ASN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 550 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1154 GLU Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1212 LYS Chi-restraints excluded: chain F residue 1259 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 110 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 143 optimal weight: 0.0370 chunk 132 optimal weight: 1.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN E 52 GLN E 53 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1026 ASN ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.224799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.164492 restraints weight = 17087.868| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 2.98 r_work: 0.4025 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.8486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13904 Z= 0.168 Angle : 0.645 16.789 18875 Z= 0.333 Chirality : 0.046 0.178 2043 Planarity : 0.004 0.042 2482 Dihedral : 5.008 57.670 1909 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.22 % Allowed : 21.99 % Favored : 73.79 % 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: -0.82 (0.20), residues: 1720 helix: 1.26 (0.28), residues: 331 sheet: -0.31 (0.21), residues: 574 loop : -1.48 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 739 HIS 0.012 0.001 HIS D 102 PHE 0.025 0.002 PHE A 440 TYR 0.042 0.002 TYR D 79 ARG 0.006 0.001 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 620) hydrogen bonds : angle 5.16349 ( 1740) SS BOND : bond 0.00679 ( 2) SS BOND : angle 2.80385 ( 4) covalent geometry : bond 0.00375 (13902) covalent geometry : angle 0.64380 (18871) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 231 time to evaluate : 1.420 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: A 152 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6392 (mptm) REVERT: A 459 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.7255 (p0) REVERT: A 741 MET cc_start: 0.7464 (ptp) cc_final: 0.6902 (ptm) REVERT: A 745 TRP cc_start: 0.7523 (p-90) cc_final: 0.7244 (p90) REVERT: A 805 ASN cc_start: 0.9017 (t0) cc_final: 0.8770 (t0) REVERT: B 32 MET cc_start: 0.6841 (mmm) cc_final: 0.6425 (mpp) REVERT: B 163 LEU cc_start: 0.8301 (mp) cc_final: 0.7970 (mt) REVERT: B 170 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: B 306 MET cc_start: 0.5875 (mtt) cc_final: 0.5572 (mtt) REVERT: B 341 ASP cc_start: 0.5697 (p0) cc_final: 0.5459 (p0) REVERT: B 343 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6872 (pm20) REVERT: B 388 TYR cc_start: 0.7928 (m-80) cc_final: 0.7396 (m-80) REVERT: D 188 ARG cc_start: 0.7101 (mmt-90) cc_final: 0.6397 (tpm170) REVERT: D 219 GLU cc_start: 0.7340 (tp30) cc_final: 0.7115 (tp30) REVERT: F 1128 HIS cc_start: 0.6223 (OUTLIER) cc_final: 0.5749 (t-90) REVERT: F 1154 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6754 (tp30) REVERT: F 1175 TYR cc_start: 0.4277 (t80) cc_final: 0.3747 (t80) REVERT: F 1224 ARG cc_start: 0.7976 (ptp90) cc_final: 0.7713 (ptp90) outliers start: 61 outliers final: 47 residues processed: 268 average time/residue: 0.2409 time to fit residues: 95.8293 Evaluate side-chains 271 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 459 ASN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1128 HIS Chi-restraints excluded: chain F residue 1154 GLU Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1212 LYS Chi-restraints excluded: chain F residue 1259 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 135 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 3 optimal weight: 50.0000 chunk 118 optimal weight: 0.0570 chunk 147 optimal weight: 0.0270 chunk 43 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN B 324 HIS ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1026 ASN ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.229174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.172672 restraints weight = 16985.864| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 3.50 r_work: 0.4056 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.8536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13904 Z= 0.111 Angle : 0.623 16.629 18875 Z= 0.316 Chirality : 0.045 0.170 2043 Planarity : 0.004 0.036 2482 Dihedral : 4.730 52.677 1909 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.73 % Allowed : 22.61 % Favored : 73.65 % 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: -0.62 (0.20), residues: 1720 helix: 1.49 (0.29), residues: 331 sheet: -0.21 (0.21), residues: 582 loop : -1.37 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 739 HIS 0.010 0.001 HIS D 102 PHE 0.021 0.001 PHE A 440 TYR 0.041 0.001 TYR D 79 ARG 0.004 0.000 ARG F1028 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 620) hydrogen bonds : angle 4.93666 ( 1740) SS BOND : bond 0.00441 ( 2) SS BOND : angle 2.32345 ( 4) covalent geometry : bond 0.00243 (13902) covalent geometry : angle 0.62246 (18871) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 1.414 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: A 152 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6374 (mptm) REVERT: A 459 ASN cc_start: 0.7553 (OUTLIER) cc_final: 0.7144 (p0) REVERT: A 737 PHE cc_start: 0.6836 (t80) cc_final: 0.6588 (t80) REVERT: A 741 MET cc_start: 0.7530 (ptp) cc_final: 0.6874 (ptm) REVERT: A 745 TRP cc_start: 0.7476 (p-90) cc_final: 0.7221 (p90) REVERT: A 797 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.5827 (t0) REVERT: A 805 ASN cc_start: 0.9009 (t0) cc_final: 0.8770 (t0) REVERT: B 32 MET cc_start: 0.6821 (mmm) cc_final: 0.6362 (mpp) REVERT: B 306 MET cc_start: 0.5673 (mtt) cc_final: 0.5372 (mtt) REVERT: B 341 ASP cc_start: 0.5667 (p0) cc_final: 0.5416 (p0) REVERT: B 343 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6131 (pm20) REVERT: B 388 TYR cc_start: 0.7818 (m-80) cc_final: 0.7487 (m-80) REVERT: D 188 ARG cc_start: 0.6962 (mmt-90) cc_final: 0.6526 (tpm170) REVERT: F 1101 LYS cc_start: 0.8293 (ttpt) cc_final: 0.7894 (ttpp) REVERT: F 1103 VAL cc_start: 0.8084 (m) cc_final: 0.7799 (t) REVERT: F 1154 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6735 (tp30) REVERT: F 1175 TYR cc_start: 0.4330 (t80) cc_final: 0.3833 (t80) REVERT: F 1218 ASP cc_start: 0.6326 (p0) cc_final: 0.5664 (p0) REVERT: F 1259 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5875 (tt) outliers start: 54 outliers final: 40 residues processed: 271 average time/residue: 0.2449 time to fit residues: 98.4947 Evaluate side-chains 273 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 459 ASN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1154 GLU Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1259 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN B 319 GLN B 350 ASN D 230 GLN E 52 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.221248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.160984 restraints weight = 17197.256| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 3.49 r_work: 0.3925 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.8836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 13904 Z= 0.245 Angle : 0.713 17.160 18875 Z= 0.369 Chirality : 0.048 0.188 2043 Planarity : 0.005 0.042 2482 Dihedral : 5.183 49.194 1909 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.36 % Allowed : 21.99 % Favored : 73.65 % 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: -0.94 (0.20), residues: 1720 helix: 1.09 (0.28), residues: 331 sheet: -0.36 (0.21), residues: 560 loop : -1.52 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 317 HIS 0.012 0.001 HIS D 102 PHE 0.025 0.002 PHE A 440 TYR 0.056 0.002 TYR D 79 ARG 0.014 0.001 ARG F1205 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 620) hydrogen bonds : angle 5.30419 ( 1740) SS BOND : bond 0.00939 ( 2) SS BOND : angle 3.27863 ( 4) covalent geometry : bond 0.00553 (13902) covalent geometry : angle 0.71196 (18871) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8806.90 seconds wall clock time: 157 minutes 30.40 seconds (9450.40 seconds total)