Starting phenix.real_space_refine on Thu May 15 15:35:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qn4_18507/05_2025/8qn4_18507.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qn4_18507/05_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_18507/05_2025/8qn4_18507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qn4_18507/05_2025/8qn4_18507.map" model { file = "/net/cci-nas-00/data/ceres_data/8qn4_18507/05_2025/8qn4_18507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qn4_18507/05_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-5687/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: 8.15, per 1000 atoms: 0.60 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: 3.10 Conformation dependent library (CDL) restraints added in 1.8 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: 1.57 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: 5.10 Time building geometry restraints manager: 3.73 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: 0.920 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: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 33.850 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.680 ------------------------------------------------------------------------------- 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 : 1.551 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: 0.3017 time to fit residues: 217.4319 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 : 1.504 ------------------------------------------------------------------------------- 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 = 0.207886 restraints weight = 17137.629| |-----------------------------------------------------------------------------| r_work (start): 0.4581 rms_B_bonded: 2.95 r_work: 0.4389 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 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 : 1.479 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: 0.7665 (m110) cc_final: 0.6892 (m110) REVERT: A 244 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7327 (mp10) REVERT: A 294 GLU cc_start: 0.6241 (mp0) cc_final: 0.6003 (mp0) REVERT: A 546 TRP cc_start: 0.5510 (t-100) cc_final: 0.5309 (t-100) REVERT: B 127 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7672 (mt-10) REVERT: B 304 ARG cc_start: 0.6905 (mtp180) cc_final: 0.6457 (ttp-110) REVERT: B 310 ILE cc_start: 0.6145 (OUTLIER) cc_final: 0.5927 (mt) REVERT: D 35 ILE cc_start: 0.6701 (mm) cc_final: 0.6489 (mm) REVERT: D 232 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7482 (pp20) REVERT: F 1023 ASN cc_start: 0.8691 (m-40) cc_final: 0.8438 (m-40) REVERT: F 1168 GLU cc_start: 0.4178 (mp0) cc_final: 0.3818 (mp0) REVERT: F 1212 LYS cc_start: 0.6069 (OUTLIER) cc_final: 0.5718 (ttpp) outliers start: 65 outliers final: 33 residues processed: 341 average time/residue: 0.2675 time to fit residues: 129.4153 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 : 1.400 ------------------------------------------------------------------------------- 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: 6.9990 chunk 129 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 136 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 85 ASN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 336 ASN B 350 ASN B 368 GLN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN E 54 GLN E 80 GLN E 89 GLN F1130 ASN F1160 HIS ** F1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1271 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.234423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.178598 restraints weight = 17074.497| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 3.88 r_work: 0.4045 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.6232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13904 Z= 0.218 Angle : 0.688 9.470 18875 Z= 0.370 Chirality : 0.046 0.176 2043 Planarity : 0.005 0.045 2482 Dihedral : 5.783 77.105 1912 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.63 % Allowed : 15.91 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.19), residues: 1720 helix: 0.81 (0.27), residues: 329 sheet: -0.24 (0.20), residues: 573 loop : -1.71 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 749 HIS 0.011 0.002 HIS D 102 PHE 0.025 0.002 PHE A 478 TYR 0.039 0.002 TYR D 79 ARG 0.007 0.001 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 620) hydrogen bonds : angle 5.75589 ( 1740) SS BOND : bond 0.00480 ( 2) SS BOND : angle 2.74987 ( 4) covalent geometry : bond 0.00451 (13902) covalent geometry : angle 0.68648 (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 332 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 265 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ASN cc_start: 0.7747 (m110) cc_final: 0.7055 (m110) REVERT: A 259 ASN cc_start: 0.8540 (m110) cc_final: 0.8202 (m-40) REVERT: A 294 GLU cc_start: 0.6327 (mp0) cc_final: 0.5806 (mp0) REVERT: A 578 TYR cc_start: 0.8407 (t80) cc_final: 0.7354 (t80) REVERT: A 797 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.6678 (t0) REVERT: A 805 ASN cc_start: 0.8651 (t0) cc_final: 0.8255 (t0) REVERT: B 163 LEU cc_start: 0.8435 (mp) cc_final: 0.8232 (mt) REVERT: B 197 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6043 (mt-10) REVERT: B 384 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7555 (p0) REVERT: D 188 ARG cc_start: 0.6489 (mmt-90) cc_final: 0.6090 (tpm170) REVERT: D 232 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7476 (pp20) REVERT: F 1212 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5405 (ttpp) REVERT: F 1257 ARG cc_start: 0.5499 (mpp80) cc_final: 0.5220 (ptp-170) REVERT: F 1274 PHE cc_start: 0.6211 (OUTLIER) cc_final: 0.5988 (m-10) outliers start: 67 outliers final: 46 residues processed: 306 average time/residue: 0.2631 time to fit residues: 116.7099 Evaluate side-chains 275 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 223 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 284 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 484 SER Chi-restraints excluded: chain A residue 511 THR 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 613 LEU Chi-restraints excluded: chain A residue 621 ILE 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 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 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 53 GLN Chi-restraints excluded: chain E residue 54 GLN 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 1130 ASN Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1212 LYS Chi-restraints excluded: chain F residue 1274 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 63 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN A 466 GLN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 350 ASN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN ** F1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1130 ASN ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1230 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 = 0.4739 r_free = 0.4739 target = 0.230192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.173363 restraints weight = 16929.079| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 3.55 r_work: 0.3997 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.6909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13904 Z= 0.198 Angle : 0.649 7.882 18875 Z= 0.345 Chirality : 0.046 0.150 2043 Planarity : 0.004 0.036 2482 Dihedral : 5.552 71.444 1911 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.60 % Allowed : 15.91 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 1720 helix: 0.91 (0.28), residues: 330 sheet: -0.21 (0.21), residues: 574 loop : -1.68 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 739 HIS 0.006 0.001 HIS D 102 PHE 0.029 0.002 PHE D 95 TYR 0.033 0.002 TYR D 79 ARG 0.004 0.001 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 620) hydrogen bonds : angle 5.54661 ( 1740) SS BOND : bond 0.00550 ( 2) SS BOND : angle 2.63430 ( 4) covalent geometry : bond 0.00432 (13902) covalent geometry : angle 0.64782 (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: 81 poor density : 252 time to evaluate : 1.531 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 545 MET cc_start: 0.7532 (mpp) cc_final: 0.7288 (mpp) REVERT: A 578 TYR cc_start: 0.8708 (t80) cc_final: 0.8495 (t80) REVERT: A 641 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7264 (mm) REVERT: A 745 TRP cc_start: 0.7514 (p-90) cc_final: 0.6815 (p90) REVERT: A 797 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.6681 (t0) REVERT: A 805 ASN cc_start: 0.8834 (t0) cc_final: 0.8497 (t0) REVERT: B 163 LEU cc_start: 0.8394 (mp) cc_final: 0.8172 (mt) REVERT: D 188 ARG cc_start: 0.6732 (mmt-90) cc_final: 0.6157 (tpm170) REVERT: D 232 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7448 (pp20) REVERT: F 1212 LYS cc_start: 0.5847 (OUTLIER) cc_final: 0.5449 (ttpp) REVERT: F 1217 LYS cc_start: 0.5360 (OUTLIER) cc_final: 0.3902 (mtmm) REVERT: F 1258 MET cc_start: 0.4282 (mmm) cc_final: 0.3871 (mmp) REVERT: F 1259 LEU cc_start: 0.6499 (mm) cc_final: 0.6037 (tt) REVERT: F 1274 PHE cc_start: 0.6465 (OUTLIER) cc_final: 0.6248 (m-10) outliers start: 81 outliers final: 52 residues processed: 296 average time/residue: 0.2598 time to fit residues: 111.5701 Evaluate side-chains 285 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 227 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 412 VAL 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 481 ASP 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 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 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 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 C residue 76 VAL 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 E residue 48 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 1065 VAL 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 1274 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 93 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 17 optimal weight: 0.0470 chunk 102 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 overall best weight: 1.3684 ------------------------------------------------------------------------------- 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 368 GLN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN ** F1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1160 HIS ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.230041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.171872 restraints weight = 17020.246| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 3.56 r_work: 0.3988 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.7319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13904 Z= 0.156 Angle : 0.612 8.847 18875 Z= 0.323 Chirality : 0.045 0.147 2043 Planarity : 0.004 0.034 2482 Dihedral : 5.248 67.325 1909 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.91 % Allowed : 18.19 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.19), residues: 1720 helix: 1.17 (0.28), residues: 331 sheet: -0.12 (0.21), residues: 577 loop : -1.58 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 183 HIS 0.013 0.001 HIS D 102 PHE 0.027 0.002 PHE D 95 TYR 0.026 0.001 TYR D 79 ARG 0.004 0.001 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 620) hydrogen bonds : angle 5.34461 ( 1740) SS BOND : bond 0.00487 ( 2) SS BOND : angle 2.41110 ( 4) covalent geometry : bond 0.00343 (13902) covalent geometry : angle 0.61088 (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 315 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 244 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7446 (p0) REVERT: A 545 MET cc_start: 0.7578 (mpp) cc_final: 0.7374 (mpp) REVERT: A 745 TRP cc_start: 0.7506 (p-90) cc_final: 0.7080 (p90) REVERT: A 797 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.6278 (t0) REVERT: A 805 ASN cc_start: 0.8985 (t0) cc_final: 0.8681 (t0) REVERT: B 163 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8066 (mt) REVERT: B 332 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7540 (mt) REVERT: D 184 TYR cc_start: 0.5641 (m-10) cc_final: 0.5405 (m-10) REVERT: D 188 ARG cc_start: 0.6654 (mmt-90) cc_final: 0.6037 (tpm170) REVERT: D 232 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7398 (pp20) REVERT: E 50 MET cc_start: 0.7637 (ttm) cc_final: 0.7417 (ttm) REVERT: E 73 TRP cc_start: 0.8091 (m-10) cc_final: 0.7805 (m-10) REVERT: F 1144 TYR cc_start: 0.7909 (t80) cc_final: 0.7680 (t80) REVERT: F 1168 GLU cc_start: 0.5308 (mp0) cc_final: 0.4890 (mp0) REVERT: F 1212 LYS cc_start: 0.5809 (OUTLIER) cc_final: 0.5416 (ttpt) REVERT: F 1217 LYS cc_start: 0.5327 (OUTLIER) cc_final: 0.3748 (mtmm) REVERT: F 1259 LEU cc_start: 0.6484 (mm) cc_final: 0.6125 (tt) outliers start: 71 outliers final: 51 residues processed: 284 average time/residue: 0.2388 time to fit residues: 99.8794 Evaluate side-chains 281 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 223 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 254 ILE 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 412 VAL 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 529 LEU 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 741 MET 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 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 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 387 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 76 VAL 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 232 GLU Chi-restraints excluded: chain E residue 36 ASN 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 Chi-restraints excluded: chain F residue 1217 LYS Chi-restraints excluded: chain F residue 1290 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 134 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 166 optimal weight: 30.0000 chunk 84 optimal weight: 6.9990 chunk 31 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 213 ASN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** F1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.230249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.173254 restraints weight = 17025.714| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 3.36 r_work: 0.4034 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.7607 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= 0.144 Angle : 0.604 10.534 18875 Z= 0.318 Chirality : 0.044 0.146 2043 Planarity : 0.004 0.034 2482 Dihedral : 5.068 64.403 1909 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.98 % Allowed : 18.81 % Favored : 76.21 % 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: -0.70 (0.20), residues: 1720 helix: 1.38 (0.29), residues: 327 sheet: -0.11 (0.21), residues: 579 loop : -1.51 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 183 HIS 0.010 0.001 HIS D 102 PHE 0.022 0.002 PHE D 95 TYR 0.037 0.001 TYR D 79 ARG 0.007 0.000 ARG F1205 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 620) hydrogen bonds : angle 5.18781 ( 1740) SS BOND : bond 0.00498 ( 2) SS BOND : angle 2.35744 ( 4) covalent geometry : bond 0.00317 (13902) covalent geometry : angle 0.60261 (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 313 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 241 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7233 (p0) REVERT: A 745 TRP cc_start: 0.7442 (p-90) cc_final: 0.7119 (p90) REVERT: A 797 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.6329 (t0) REVERT: A 805 ASN cc_start: 0.9008 (t0) cc_final: 0.8701 (t0) REVERT: B 163 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8015 (mt) REVERT: B 332 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7616 (mt) REVERT: D 188 ARG cc_start: 0.6677 (mmt-90) cc_final: 0.6131 (tpm170) REVERT: D 232 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7442 (pp20) REVERT: F 1168 GLU cc_start: 0.5339 (mp0) cc_final: 0.5084 (mp0) REVERT: F 1212 LYS cc_start: 0.5822 (OUTLIER) cc_final: 0.5443 (ttpt) REVERT: F 1258 MET cc_start: 0.4326 (mmm) cc_final: 0.4004 (mmp) REVERT: F 1259 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.5989 (tt) outliers start: 72 outliers final: 52 residues processed: 279 average time/residue: 0.2680 time to fit residues: 108.7629 Evaluate side-chains 283 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 224 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 254 ILE Chi-restraints excluded: chain A residue 256 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 412 VAL 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 529 LEU 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 741 MET 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 97 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 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 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 C residue 76 VAL 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 232 GLU 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 1128 HIS 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: 3.9990 chunk 55 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 123 optimal weight: 0.9990 chunk 157 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN B 85 ASN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN ** F1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.227289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.171622 restraints weight = 16976.012| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 3.40 r_work: 0.3993 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.8026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13904 Z= 0.177 Angle : 0.638 12.304 18875 Z= 0.336 Chirality : 0.045 0.143 2043 Planarity : 0.004 0.037 2482 Dihedral : 5.107 60.996 1909 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.84 % Allowed : 19.09 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1720 helix: 1.30 (0.29), residues: 330 sheet: -0.22 (0.21), residues: 584 loop : -1.56 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 183 HIS 0.010 0.001 HIS D 102 PHE 0.021 0.002 PHE D 95 TYR 0.036 0.002 TYR D 79 ARG 0.006 0.001 ARG F1205 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 620) hydrogen bonds : angle 5.19588 ( 1740) SS BOND : bond 0.00630 ( 2) SS BOND : angle 2.57684 ( 4) covalent geometry : bond 0.00392 (13902) covalent geometry : angle 0.63666 (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: 70 poor density : 239 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.6858 (OUTLIER) cc_final: 0.6289 (mptm) REVERT: A 459 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7484 (p0) REVERT: A 711 MET cc_start: 0.6273 (ppp) cc_final: 0.6055 (ppp) REVERT: A 745 TRP cc_start: 0.7501 (p-90) cc_final: 0.7254 (p90) REVERT: A 786 SER cc_start: 0.8518 (p) cc_final: 0.6913 (p) REVERT: A 797 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.6233 (t0) REVERT: A 805 ASN cc_start: 0.9062 (t0) cc_final: 0.8738 (t0) REVERT: B 163 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8029 (mt) REVERT: B 306 MET cc_start: 0.5706 (mtt) cc_final: 0.5434 (mtt) REVERT: B 388 TYR cc_start: 0.7843 (m-80) cc_final: 0.7475 (m-80) REVERT: D 184 TYR cc_start: 0.5677 (m-10) cc_final: 0.5439 (m-10) REVERT: D 188 ARG cc_start: 0.6951 (mmt-90) cc_final: 0.6191 (tpm170) REVERT: D 232 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7378 (pp20) REVERT: E 54 GLN cc_start: 0.8406 (pt0) cc_final: 0.8198 (pt0) REVERT: F 1175 TYR cc_start: 0.4414 (t80) cc_final: 0.3885 (t80) REVERT: F 1212 LYS cc_start: 0.5845 (OUTLIER) cc_final: 0.5398 (ttpt) REVERT: F 1217 LYS cc_start: 0.5750 (OUTLIER) cc_final: 0.3865 (mtmm) REVERT: F 1224 ARG cc_start: 0.8024 (ptp90) cc_final: 0.7700 (ptp90) REVERT: F 1269 ARG cc_start: 0.8199 (mpp80) cc_final: 0.7965 (mpt-90) outliers start: 70 outliers final: 55 residues processed: 278 average time/residue: 0.2399 time to fit residues: 97.8039 Evaluate side-chains 288 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 226 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 325 MET 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 412 VAL 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 463 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 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 619 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 741 MET 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 97 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 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 69 VAL 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 50 MET 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 1210 VAL Chi-restraints excluded: chain F residue 1212 LYS Chi-restraints excluded: chain F residue 1217 LYS Chi-restraints excluded: chain F residue 1290 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 33 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 350 ASN ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1024 ASN ** F1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4672 r_free = 0.4672 target = 0.222581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.163417 restraints weight = 16870.642| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 3.41 r_work: 0.3890 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.8577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 13904 Z= 0.248 Angle : 0.698 9.502 18875 Z= 0.369 Chirality : 0.048 0.176 2043 Planarity : 0.004 0.052 2482 Dihedral : 5.437 58.185 1909 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.05 % Allowed : 20.12 % Favored : 74.83 % 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: -1.07 (0.19), residues: 1720 helix: 0.95 (0.28), residues: 334 sheet: -0.43 (0.20), residues: 584 loop : -1.65 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 183 HIS 0.012 0.002 HIS D 102 PHE 0.022 0.002 PHE B 259 TYR 0.037 0.002 TYR D 79 ARG 0.008 0.001 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 620) hydrogen bonds : angle 5.50610 ( 1740) SS BOND : bond 0.00924 ( 2) SS BOND : angle 3.12383 ( 4) covalent geometry : bond 0.00556 (13902) covalent geometry : angle 0.69645 (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 307 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 234 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6298 (mptm) REVERT: A 459 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7665 (p0) REVERT: A 711 MET cc_start: 0.6429 (ppp) cc_final: 0.6193 (ppp) REVERT: A 745 TRP cc_start: 0.7595 (p-90) cc_final: 0.7224 (p90) REVERT: A 805 ASN cc_start: 0.9042 (t0) cc_final: 0.8729 (t0) REVERT: B 163 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8151 (mt) REVERT: B 306 MET cc_start: 0.6115 (mtt) cc_final: 0.5636 (mtt) REVERT: B 345 TYR cc_start: 0.6378 (OUTLIER) cc_final: 0.6129 (m-10) REVERT: D 184 TYR cc_start: 0.5893 (m-10) cc_final: 0.5606 (m-10) REVERT: D 188 ARG cc_start: 0.7362 (mmt-90) cc_final: 0.6276 (tpm170) REVERT: D 219 GLU cc_start: 0.7649 (tp30) cc_final: 0.7358 (tp30) REVERT: D 232 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7355 (pp20) REVERT: E 54 GLN cc_start: 0.8426 (pt0) cc_final: 0.8223 (pt0) REVERT: F 1175 TYR cc_start: 0.4628 (t80) cc_final: 0.3344 (t80) REVERT: F 1212 LYS cc_start: 0.5989 (OUTLIER) cc_final: 0.5583 (ttpt) REVERT: F 1217 LYS cc_start: 0.5848 (OUTLIER) cc_final: 0.3870 (mtmm) REVERT: F 1224 ARG cc_start: 0.8120 (ptp90) cc_final: 0.7806 (ptp90) REVERT: F 1259 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.5945 (tt) outliers start: 73 outliers final: 53 residues processed: 278 average time/residue: 0.2451 time to fit residues: 100.3012 Evaluate side-chains 289 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 228 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 325 MET 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 412 VAL 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 461 THR Chi-restraints excluded: chain A residue 463 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 571 THR 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 50 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 163 LEU 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 261 LEU Chi-restraints excluded: chain B residue 281 ARG 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 B residue 391 THR 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 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 50 MET Chi-restraints excluded: chain E residue 76 VAL 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 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 1290 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 110 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 446 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN B 347 HIS ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4750 r_free = 0.4750 target = 0.226460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.182222 restraints weight = 16968.472| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 4.49 r_work: 0.3967 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.8619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13904 Z= 0.132 Angle : 0.641 15.396 18875 Z= 0.329 Chirality : 0.045 0.170 2043 Planarity : 0.004 0.036 2482 Dihedral : 4.982 53.601 1909 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.22 % Allowed : 21.30 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.44 (0.29), residues: 332 sheet: -0.38 (0.20), residues: 593 loop : -1.52 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 183 HIS 0.007 0.001 HIS D 102 PHE 0.023 0.001 PHE A 440 TYR 0.040 0.001 TYR D 79 ARG 0.006 0.000 ARG F1205 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 620) hydrogen bonds : angle 5.15176 ( 1740) SS BOND : bond 0.00531 ( 2) SS BOND : angle 2.57935 ( 4) covalent geometry : bond 0.00297 (13902) covalent geometry : angle 0.64009 (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 312 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 251 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6373 (mptm) REVERT: A 368 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7860 (mm-30) REVERT: A 412 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8442 (m) REVERT: A 459 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7472 (p0) REVERT: A 745 TRP cc_start: 0.7627 (p-90) cc_final: 0.7337 (p90) REVERT: A 805 ASN cc_start: 0.9005 (t0) cc_final: 0.8690 (t0) REVERT: B 170 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: B 306 MET cc_start: 0.6036 (mtt) cc_final: 0.5753 (mtt) REVERT: B 388 TYR cc_start: 0.7910 (m-80) cc_final: 0.7437 (m-80) REVERT: D 32 PRO cc_start: 0.6081 (Cg_endo) cc_final: 0.5824 (Cg_exo) REVERT: D 188 ARG cc_start: 0.7151 (mmt-90) cc_final: 0.6458 (tpm170) REVERT: D 219 GLU cc_start: 0.7556 (tp30) cc_final: 0.7340 (tp30) REVERT: D 232 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7556 (pp20) REVERT: E 73 TRP cc_start: 0.8021 (m-10) cc_final: 0.7721 (m-10) REVERT: F 1128 HIS cc_start: 0.6540 (OUTLIER) cc_final: 0.5720 (t-90) REVERT: F 1175 TYR cc_start: 0.4387 (t80) cc_final: 0.3850 (t80) REVERT: F 1212 LYS cc_start: 0.6299 (OUTLIER) cc_final: 0.5915 (ttpt) REVERT: F 1224 ARG cc_start: 0.8013 (ptp90) cc_final: 0.7751 (ptp90) REVERT: F 1259 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6082 (tt) outliers start: 61 outliers final: 46 residues processed: 285 average time/residue: 0.2473 time to fit residues: 104.1804 Evaluate side-chains 283 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 256 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 325 MET 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 412 VAL 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 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 B residue 50 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 170 GLN 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 261 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 327 LEU 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 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 76 VAL Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1128 HIS 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: 7.9990 chunk 138 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 3 optimal weight: 50.0000 chunk 118 optimal weight: 0.8980 chunk 147 optimal weight: 0.4980 chunk 43 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN B 324 HIS ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.224954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.164008 restraints weight = 16970.866| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 3.28 r_work: 0.4003 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.8785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13904 Z= 0.149 Angle : 0.657 17.074 18875 Z= 0.337 Chirality : 0.046 0.179 2043 Planarity : 0.004 0.036 2482 Dihedral : 4.938 49.072 1909 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.08 % Allowed : 21.92 % Favored : 74.00 % 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: -0.81 (0.20), residues: 1720 helix: 1.36 (0.29), residues: 333 sheet: -0.36 (0.21), residues: 587 loop : -1.48 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 776 HIS 0.006 0.001 HIS D 102 PHE 0.025 0.002 PHE A 440 TYR 0.041 0.002 TYR D 79 ARG 0.006 0.000 ARG F1205 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 620) hydrogen bonds : angle 5.14322 ( 1740) SS BOND : bond 0.00663 ( 2) SS BOND : angle 2.75573 ( 4) covalent geometry : bond 0.00340 (13902) covalent geometry : angle 0.65536 (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 290 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 231 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.6843 (OUTLIER) cc_final: 0.6338 (mptm) REVERT: A 459 ASN cc_start: 0.7705 (OUTLIER) cc_final: 0.7335 (p0) REVERT: A 578 TYR cc_start: 0.8499 (t80) cc_final: 0.7588 (t80) REVERT: A 745 TRP cc_start: 0.7511 (p-90) cc_final: 0.7221 (p90) REVERT: A 805 ASN cc_start: 0.8988 (t0) cc_final: 0.8705 (t0) REVERT: B 32 MET cc_start: 0.6875 (mmm) cc_final: 0.6463 (mpp) REVERT: B 170 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7999 (mp10) REVERT: B 306 MET cc_start: 0.5864 (mtt) cc_final: 0.5615 (mtt) REVERT: B 388 TYR cc_start: 0.7838 (m-80) cc_final: 0.7523 (m-80) REVERT: D 32 PRO cc_start: 0.6250 (Cg_endo) cc_final: 0.5986 (Cg_exo) REVERT: D 188 ARG cc_start: 0.7128 (mmt-90) cc_final: 0.6497 (tpm170) REVERT: D 232 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7420 (pp20) REVERT: F 1128 HIS cc_start: 0.6512 (OUTLIER) cc_final: 0.5817 (t-90) REVERT: F 1175 TYR cc_start: 0.4447 (t80) cc_final: 0.3907 (t80) REVERT: F 1224 ARG cc_start: 0.7957 (ptp90) cc_final: 0.7685 (ptp90) REVERT: F 1259 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.5939 (tt) outliers start: 59 outliers final: 50 residues processed: 267 average time/residue: 0.2597 time to fit residues: 104.2382 Evaluate side-chains 277 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 221 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 325 MET 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 446 GLN 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 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 B residue 50 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 GLN 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 261 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 327 LEU 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 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 76 VAL 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 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 34 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 116 optimal weight: 0.0020 chunk 14 optimal weight: 30.0000 chunk 73 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.224448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.162758 restraints weight = 17068.568| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 3.41 r_work: 0.3982 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.8831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 13904 Z= 0.209 Angle : 0.903 59.186 18875 Z= 0.495 Chirality : 0.049 0.632 2043 Planarity : 0.004 0.036 2482 Dihedral : 4.932 49.049 1909 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.36 % Allowed : 21.65 % Favored : 74.00 % Cbeta Deviations : 0.06 % 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 (0.20), residues: 1720 helix: 1.33 (0.29), residues: 333 sheet: -0.38 (0.20), residues: 591 loop : -1.50 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 776 HIS 0.005 0.001 HIS D 102 PHE 0.033 0.002 PHE E 68 TYR 0.060 0.002 TYR A 578 ARG 0.005 0.000 ARG F1205 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 620) hydrogen bonds : angle 5.15851 ( 1740) SS BOND : bond 0.00795 ( 2) SS BOND : angle 2.79630 ( 4) covalent geometry : bond 0.00478 (13902) covalent geometry : angle 0.90195 (18871) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7981.65 seconds wall clock time: 138 minutes 31.42 seconds (8311.42 seconds total)