Starting phenix.real_space_refine on Sat Oct 11 08:51:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qn4_18507/10_2025/8qn4_18507.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qn4_18507/10_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_18507/10_2025/8qn4_18507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qn4_18507/10_2025/8qn4_18507.map" model { file = "/net/cci-nas-00/data/ceres_data/8qn4_18507/10_2025/8qn4_18507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qn4_18507/10_2025/8qn4_18507.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'ARG: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: 2.99, per 1000 atoms: 0.22 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: 0.99 Conformation dependent library (CDL) restraints added in 612.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.49 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: 2.79 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2922 1.34 - 1.46: 4941 1.46 - 1.59: 5965 1.59 - 1.72: 0 1.72 - 1.84: 74 Bond restraints: 13902 Sorted by residual: bond pdb=" CA VAL B 286 " pdb=" C VAL B 286 " ideal model delta sigma weight residual 1.524 1.465 0.060 1.06e-02 8.90e+03 3.17e+01 bond pdb=" CA GLY B 210 " pdb=" C GLY B 210 " ideal model delta sigma weight residual 1.517 1.467 0.050 9.60e-03 1.09e+04 2.72e+01 bond pdb=" CA TYR D 62 " pdb=" CB TYR D 62 " ideal model delta sigma weight residual 1.527 1.576 -0.049 1.05e-02 9.07e+03 2.18e+01 bond pdb=" CA GLY F1211 " pdb=" C GLY F1211 " ideal model delta sigma weight residual 1.513 1.467 0.046 1.08e-02 8.57e+03 1.79e+01 bond pdb=" CA SER A 657 " pdb=" C SER A 657 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.28e-02 6.10e+03 1.74e+01 ... (remaining 13897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 17285 3.61 - 7.21: 1497 7.21 - 10.82: 82 10.82 - 14.42: 5 14.42 - 18.03: 2 Bond angle restraints: 18871 Sorted by residual: angle pdb=" N GLY B 196 " pdb=" CA GLY B 196 " pdb=" C GLY B 196 " ideal model delta sigma weight residual 112.04 94.01 18.03 1.02e+00 9.61e-01 3.12e+02 angle pdb=" C VAL B 286 " pdb=" CA VAL B 286 " pdb=" CB VAL B 286 " ideal model delta sigma weight residual 111.05 102.79 8.26 8.90e-01 1.26e+00 8.61e+01 angle pdb=" CA ASP A 493 " pdb=" CB ASP A 493 " pdb=" CG ASP A 493 " ideal model delta sigma weight residual 112.60 121.22 -8.62 1.00e+00 1.00e+00 7.43e+01 angle pdb=" CA ASN B 287 " pdb=" CB ASN B 287 " pdb=" CG ASN B 287 " ideal model delta sigma weight residual 112.60 104.15 8.45 1.00e+00 1.00e+00 7.14e+01 angle pdb=" N SER D 242 " pdb=" CA SER D 242 " pdb=" C SER D 242 " ideal model delta sigma weight residual 110.80 128.19 -17.39 2.13e+00 2.20e-01 6.66e+01 ... (remaining 18866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.76: 7655 18.76 - 37.51: 367 37.51 - 56.27: 77 56.27 - 75.02: 54 75.02 - 93.78: 28 Dihedral angle restraints: 8181 sinusoidal: 3186 harmonic: 4995 Sorted by residual: dihedral pdb=" CA LYS B 280 " pdb=" C LYS B 280 " pdb=" N ARG B 281 " pdb=" CA ARG B 281 " ideal model delta harmonic sigma weight residual 180.00 135.24 44.76 0 5.00e+00 4.00e-02 8.01e+01 dihedral pdb=" N SER D 243 " pdb=" C SER D 243 " pdb=" CA SER D 243 " pdb=" CB SER D 243 " ideal model delta harmonic sigma weight residual 122.80 140.97 -18.17 0 2.50e+00 1.60e-01 5.28e+01 dihedral pdb=" N SER D 242 " pdb=" C SER D 242 " pdb=" CA SER D 242 " pdb=" CB SER D 242 " ideal model delta harmonic sigma weight residual 122.80 139.91 -17.11 0 2.50e+00 1.60e-01 4.68e+01 ... (remaining 8178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 1705 0.158 - 0.317: 308 0.317 - 0.475: 25 0.475 - 0.634: 4 0.634 - 0.792: 1 Chirality restraints: 2043 Sorted by residual: chirality pdb=" CA SER D 242 " pdb=" N SER D 242 " pdb=" C SER D 242 " pdb=" CB SER D 242 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" CA ARG F1269 " pdb=" N ARG F1269 " pdb=" C ARG F1269 " pdb=" CB ARG F1269 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" CA SER D 243 " pdb=" N SER D 243 " pdb=" C SER D 243 " pdb=" CB SER D 243 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.02e+00 ... (remaining 2040 not shown) Planarity restraints: 2482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 686 " 0.151 2.00e-02 2.50e+03 1.22e-01 2.99e+02 pdb=" CG TYR A 686 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 686 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR A 686 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 TYR A 686 " -0.155 2.00e-02 2.50e+03 pdb=" CE2 TYR A 686 " -0.093 2.00e-02 2.50e+03 pdb=" CZ TYR A 686 " -0.045 2.00e-02 2.50e+03 pdb=" OH TYR A 686 " 0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 255 " -0.216 2.00e-02 2.50e+03 1.12e-01 2.53e+02 pdb=" CG TYR A 255 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR A 255 " 0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR A 255 " 0.124 2.00e-02 2.50e+03 pdb=" CE1 TYR A 255 " 0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR A 255 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 255 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 255 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F1274 " -0.132 2.00e-02 2.50e+03 1.02e-01 1.83e+02 pdb=" CG PHE F1274 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE F1274 " 0.183 2.00e-02 2.50e+03 pdb=" CD2 PHE F1274 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE F1274 " -0.084 2.00e-02 2.50e+03 pdb=" CE2 PHE F1274 " 0.043 2.00e-02 2.50e+03 pdb=" CZ PHE F1274 " -0.097 2.00e-02 2.50e+03 ... (remaining 2479 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1240 2.75 - 3.29: 12249 3.29 - 3.82: 21911 3.82 - 4.36: 27852 4.36 - 4.90: 46384 Nonbonded interactions: 109636 Sorted by model distance: nonbonded pdb=" N GLY B 196 " pdb=" O GLY B 196 " model vdw 2.210 2.496 nonbonded pdb=" N THR F1162 " pdb=" O THR F1162 " model vdw 2.405 2.496 nonbonded pdb=" N TYR A 432 " pdb=" O TYR A 432 " model vdw 2.438 2.496 nonbonded pdb=" N SER B 126 " pdb=" O SER B 126 " model vdw 2.453 2.496 nonbonded pdb=" N GLY A 638 " pdb=" O GLY A 638 " model vdw 2.461 2.496 ... (remaining 109631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.340 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.050 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.057 0.004 ARG F1224 TYR 0.230 0.030 TYR A 686 PHE 0.183 0.020 PHE F1274 TRP 0.167 0.024 TRP B 183 HIS 0.025 0.006 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.01672 (13902) covalent geometry : angle 2.07952 (18871) SS BOND : bond 0.00437 ( 2) SS BOND : angle 6.69989 ( 4) hydrogen bonds : bond 0.25438 ( 620) hydrogen bonds : angle 9.60040 ( 1740) *********************** 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 : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.1379 time to fit residues: 98.9823 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 : 0.503 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0050 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- 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 225 GLN B 319 GLN B 350 ASN D 54 GLN D 60 ASN 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.247915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.196012 restraints weight = 17208.936| |-----------------------------------------------------------------------------| r_work (start): 0.4489 rms_B_bonded: 3.30 r_work: 0.4352 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 13904 Z= 0.192 Angle : 0.705 9.110 18875 Z= 0.382 Chirality : 0.048 0.162 2043 Planarity : 0.005 0.042 2482 Dihedral : 6.198 75.616 1921 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.63 % Allowed : 11.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.18), residues: 1720 helix: 0.53 (0.27), residues: 322 sheet: -0.23 (0.20), residues: 582 loop : -1.95 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 421 TYR 0.038 0.002 TYR D 79 PHE 0.028 0.002 PHE A 565 TRP 0.023 0.002 TRP B 93 HIS 0.013 0.002 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00396 (13902) covalent geometry : angle 0.70404 (18871) SS BOND : bond 0.00041 ( 2) SS BOND : angle 2.04276 ( 4) hydrogen bonds : bond 0.04502 ( 620) hydrogen bonds : angle 6.37750 ( 1740) *********************** 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 363 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 296 time to evaluate : 0.500 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: 0.7840 (m110) cc_final: 0.7095 (m110) REVERT: A 197 PHE cc_start: 0.7311 (m-80) cc_final: 0.7067 (m-80) REVERT: A 280 HIS cc_start: 0.7047 (m90) cc_final: 0.6732 (m90) REVERT: A 546 TRP cc_start: 0.5461 (t-100) cc_final: 0.5222 (t-100) REVERT: B 82 LYS cc_start: 0.7804 (mmtt) cc_final: 0.7590 (ttpt) REVERT: B 127 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7845 (mt-10) REVERT: B 304 ARG cc_start: 0.6922 (mtp180) cc_final: 0.6493 (ttp-110) REVERT: B 310 ILE cc_start: 0.6222 (OUTLIER) cc_final: 0.5948 (mt) REVERT: D 35 ILE cc_start: 0.6713 (mm) cc_final: 0.6500 (mm) REVERT: D 232 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7177 (tp30) REVERT: F 1023 ASN cc_start: 0.8668 (m-40) cc_final: 0.8350 (m-40) REVERT: F 1212 LYS cc_start: 0.5981 (OUTLIER) cc_final: 0.5700 (ttpp) outliers start: 67 outliers final: 34 residues processed: 337 average time/residue: 0.1225 time to fit residues: 59.0929 Evaluate side-chains 280 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 243 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 357 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 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 51 optimal weight: 3.9990 chunk 116 optimal weight: 0.0570 chunk 62 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 63 optimal weight: 0.0670 chunk 49 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.2242 ------------------------------------------------------------------------------- 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 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 E 54 GLN E 80 GLN E 89 GLN ** F1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1130 ASN F1160 HIS ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1271 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.233200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.172707 restraints weight = 17019.351| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 3.61 r_work: 0.4055 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 13904 Z= 0.228 Angle : 0.699 9.104 18875 Z= 0.374 Chirality : 0.046 0.161 2043 Planarity : 0.005 0.049 2482 Dihedral : 5.832 77.643 1912 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.84 % Allowed : 15.77 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.19), residues: 1720 helix: 0.78 (0.28), residues: 324 sheet: -0.24 (0.20), residues: 568 loop : -1.76 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 188 TYR 0.034 0.002 TYR D 79 PHE 0.024 0.002 PHE A 478 TRP 0.024 0.002 TRP A 749 HIS 0.014 0.002 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00497 (13902) covalent geometry : angle 0.69797 (18871) SS BOND : bond 0.00548 ( 2) SS BOND : angle 2.82903 ( 4) hydrogen bonds : bond 0.04110 ( 620) hydrogen bonds : angle 5.83548 ( 1740) *********************** 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: 70 poor density : 262 time to evaluate : 0.463 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 177 ILE cc_start: 0.7823 (mm) cc_final: 0.7490 (mm) REVERT: A 181 ASN cc_start: 0.7700 (m110) cc_final: 0.7044 (m110) REVERT: A 197 PHE cc_start: 0.7750 (m-80) cc_final: 0.7456 (m-80) REVERT: A 202 GLU cc_start: 0.7012 (pp20) cc_final: 0.6765 (pp20) REVERT: A 259 ASN cc_start: 0.8559 (m110) cc_final: 0.8216 (m-40) REVERT: A 432 TYR cc_start: 0.6246 (t80) cc_final: 0.5985 (m-80) REVERT: A 797 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.6657 (t0) REVERT: A 805 ASN cc_start: 0.8697 (t0) cc_final: 0.8300 (t0) REVERT: B 82 LYS cc_start: 0.7745 (mmtt) cc_final: 0.7435 (ttpt) REVERT: D 188 ARG cc_start: 0.6579 (mmt-90) cc_final: 0.6101 (tpm170) REVERT: D 232 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7323 (pp20) REVERT: E 107 LYS cc_start: 0.7233 (mtmm) cc_final: 0.7018 (mtmm) REVERT: F 1212 LYS cc_start: 0.5813 (OUTLIER) cc_final: 0.5324 (ttpp) REVERT: F 1274 PHE cc_start: 0.6245 (OUTLIER) cc_final: 0.6019 (m-10) outliers start: 70 outliers final: 51 residues processed: 307 average time/residue: 0.1152 time to fit residues: 51.9602 Evaluate side-chains 281 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 226 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 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 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 110 LEU 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 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 1110 SER 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 161 optimal weight: 8.9990 chunk 159 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 446 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN A 803 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 334 ASN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN D 230 GLN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.222161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.160675 restraints weight = 17021.157| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 3.43 r_work: 0.3896 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.7634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 13904 Z= 0.313 Angle : 0.781 8.513 18875 Z= 0.420 Chirality : 0.050 0.231 2043 Planarity : 0.006 0.071 2482 Dihedral : 6.200 73.637 1911 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 6.02 % Allowed : 17.15 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.19), residues: 1720 helix: 0.15 (0.27), residues: 339 sheet: -0.47 (0.21), residues: 570 loop : -1.91 (0.19), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 188 TYR 0.042 0.003 TYR D 222 PHE 0.028 0.003 PHE D 95 TRP 0.021 0.003 TRP A 749 HIS 0.010 0.002 HIS B 121 Details of bonding type rmsd covalent geometry : bond 0.00693 (13902) covalent geometry : angle 0.77932 (18871) SS BOND : bond 0.00916 ( 2) SS BOND : angle 3.36689 ( 4) hydrogen bonds : bond 0.04337 ( 620) hydrogen bonds : angle 6.01176 ( 1740) *********************** 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 339 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 252 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.6784 (OUTLIER) cc_final: 0.6227 (mptm) REVERT: A 197 PHE cc_start: 0.7968 (m-80) cc_final: 0.7589 (m-80) REVERT: A 440 PHE cc_start: 0.7097 (t80) cc_final: 0.6877 (t80) REVERT: A 459 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7720 (p0) REVERT: A 745 TRP cc_start: 0.7666 (p-90) cc_final: 0.7220 (p90) REVERT: A 786 SER cc_start: 0.8629 (p) cc_final: 0.7386 (m) REVERT: A 797 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.5980 (t70) REVERT: A 805 ASN cc_start: 0.8979 (t0) cc_final: 0.8596 (t0) REVERT: B 183 TRP cc_start: 0.7587 (p-90) cc_final: 0.7265 (p-90) REVERT: B 306 MET cc_start: 0.6067 (mtt) cc_final: 0.5847 (mtt) REVERT: D 184 TYR cc_start: 0.5853 (m-10) cc_final: 0.5649 (m-10) REVERT: D 188 ARG cc_start: 0.7306 (mmt-90) cc_final: 0.6157 (tpm170) REVERT: D 232 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7240 (pp20) REVERT: F 1212 LYS cc_start: 0.6040 (OUTLIER) cc_final: 0.5625 (tttt) REVERT: F 1217 LYS cc_start: 0.6067 (OUTLIER) cc_final: 0.4525 (mtmm) REVERT: F 1224 ARG cc_start: 0.8211 (ptp90) cc_final: 0.7800 (ptp90) REVERT: F 1257 ARG cc_start: 0.5962 (mpp80) cc_final: 0.5682 (ptp-170) REVERT: F 1258 MET cc_start: 0.4345 (mmm) cc_final: 0.4019 (mmp) REVERT: F 1259 LEU cc_start: 0.6521 (mm) cc_final: 0.5977 (tt) outliers start: 87 outliers final: 59 residues processed: 306 average time/residue: 0.1157 time to fit residues: 52.2613 Evaluate side-chains 288 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 223 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 291 GLU 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 461 THR 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 673 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 760 TYR 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 156 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 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 71 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1085 THR Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1128 HIS Chi-restraints excluded: chain F residue 1172 GLU Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1212 LYS Chi-restraints excluded: chain F residue 1217 LYS Chi-restraints excluded: chain F residue 1274 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 38 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 14 optimal weight: 30.0000 chunk 90 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 141 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 448 ASN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN B 347 HIS B 368 GLN E 53 GLN F1026 ASN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.227717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.173408 restraints weight = 16871.749| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 3.44 r_work: 0.3985 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.7783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13904 Z= 0.140 Angle : 0.610 8.524 18875 Z= 0.323 Chirality : 0.045 0.147 2043 Planarity : 0.004 0.034 2482 Dihedral : 5.350 70.767 1909 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.63 % Allowed : 19.71 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.19), residues: 1720 helix: 1.02 (0.28), residues: 331 sheet: -0.39 (0.20), residues: 594 loop : -1.71 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 212 TYR 0.024 0.001 TYR A 229 PHE 0.030 0.002 PHE D 95 TRP 0.021 0.002 TRP A 776 HIS 0.014 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00304 (13902) covalent geometry : angle 0.60957 (18871) SS BOND : bond 0.00369 ( 2) SS BOND : angle 2.24081 ( 4) hydrogen bonds : bond 0.03380 ( 620) hydrogen bonds : angle 5.38274 ( 1740) *********************** 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 321 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 254 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.6792 (OUTLIER) cc_final: 0.6263 (mptm) REVERT: A 396 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8000 (mt-10) REVERT: A 412 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8352 (m) REVERT: A 421 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7796 (ttm110) REVERT: A 545 MET cc_start: 0.7490 (mpp) cc_final: 0.7215 (mpp) REVERT: A 711 MET cc_start: 0.6183 (ppp) cc_final: 0.5937 (ppp) REVERT: A 745 TRP cc_start: 0.7515 (p-90) cc_final: 0.7119 (p90) REVERT: A 797 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.6008 (t0) REVERT: A 805 ASN cc_start: 0.9022 (t0) cc_final: 0.8663 (t0) REVERT: B 183 TRP cc_start: 0.7508 (p-90) cc_final: 0.7193 (p-90) REVERT: B 306 MET cc_start: 0.5680 (mtt) cc_final: 0.5384 (mtt) REVERT: B 332 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7544 (mt) REVERT: D 188 ARG cc_start: 0.6913 (mmt-90) cc_final: 0.6044 (tpm170) REVERT: D 232 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7454 (pp20) REVERT: F 1129 ASP cc_start: 0.7527 (t70) cc_final: 0.6977 (p0) REVERT: F 1154 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6310 (tp30) REVERT: F 1224 ARG cc_start: 0.8009 (ptp90) cc_final: 0.7598 (ptp90) REVERT: F 1259 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6072 (tt) REVERT: F 1290 ASN cc_start: 0.6134 (p0) cc_final: 0.5822 (p0) outliers start: 67 outliers final: 47 residues processed: 288 average time/residue: 0.1206 time to fit residues: 50.7322 Evaluate side-chains 281 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 227 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 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 412 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 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 760 TYR 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 184 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 232 GLU 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 1154 GLU Chi-restraints excluded: chain F residue 1172 GLU Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1212 LYS Chi-restraints excluded: chain F residue 1259 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.223667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.163230 restraints weight = 16868.667| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 3.43 r_work: 0.3930 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.8131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 13904 Z= 0.195 Angle : 0.644 12.145 18875 Z= 0.341 Chirality : 0.046 0.144 2043 Planarity : 0.004 0.039 2482 Dihedral : 5.393 74.907 1909 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 5.46 % Allowed : 18.88 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.19), residues: 1720 helix: 0.98 (0.28), residues: 334 sheet: -0.50 (0.20), residues: 583 loop : -1.61 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F1205 TYR 0.023 0.002 TYR D 222 PHE 0.022 0.002 PHE D 95 TRP 0.020 0.002 TRP A 749 HIS 0.011 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00432 (13902) covalent geometry : angle 0.64241 (18871) SS BOND : bond 0.00684 ( 2) SS BOND : angle 2.86499 ( 4) hydrogen bonds : bond 0.03523 ( 620) hydrogen bonds : angle 5.40198 ( 1740) *********************** 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 323 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 244 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.6778 (OUTLIER) cc_final: 0.6289 (mptm) REVERT: A 368 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7840 (mm-30) REVERT: A 477 TYR cc_start: 0.8606 (m-80) cc_final: 0.8180 (m-80) REVERT: A 745 TRP cc_start: 0.7628 (p-90) cc_final: 0.7148 (p90) REVERT: A 797 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.6111 (t70) REVERT: A 805 ASN cc_start: 0.8994 (t0) cc_final: 0.8659 (t0) REVERT: B 306 MET cc_start: 0.5904 (mtt) cc_final: 0.5563 (mtt) REVERT: B 332 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7669 (mt) REVERT: D 188 ARG cc_start: 0.7262 (mmt-90) cc_final: 0.6281 (tpm170) REVERT: D 232 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7336 (pp20) REVERT: F 1103 VAL cc_start: 0.8092 (m) cc_final: 0.7741 (t) REVERT: F 1154 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6293 (tp30) REVERT: F 1217 LYS cc_start: 0.5795 (OUTLIER) cc_final: 0.3890 (mtmm) REVERT: F 1224 ARG cc_start: 0.8061 (ptp90) cc_final: 0.7674 (ptp90) REVERT: F 1279 GLU cc_start: 0.6443 (mp0) cc_final: 0.6149 (mp0) REVERT: F 1290 ASN cc_start: 0.6110 (p0) cc_final: 0.5815 (p0) outliers start: 79 outliers final: 60 residues processed: 291 average time/residue: 0.1075 time to fit residues: 45.9567 Evaluate side-chains 292 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 226 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 152 LYS 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 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 514 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 581 LEU 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 121 HIS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 201 THR 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 332 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 ILE 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 186 THR 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 53 GLN Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1085 THR Chi-restraints excluded: chain F residue 1110 SER Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1146 THR Chi-restraints excluded: chain F residue 1154 GLU Chi-restraints excluded: chain F residue 1172 GLU Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1212 LYS Chi-restraints excluded: chain F residue 1217 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN D 241 ASN ** 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 = 0.4665 r_free = 0.4665 target = 0.221956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.161871 restraints weight = 16946.928| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 3.44 r_work: 0.3920 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.8499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13904 Z= 0.205 Angle : 0.650 10.289 18875 Z= 0.345 Chirality : 0.046 0.144 2043 Planarity : 0.004 0.042 2482 Dihedral : 5.521 82.347 1909 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.33 % Allowed : 19.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.20), residues: 1720 helix: 0.93 (0.28), residues: 333 sheet: -0.46 (0.21), residues: 574 loop : -1.62 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 421 TYR 0.032 0.002 TYR D 79 PHE 0.021 0.002 PHE D 95 TRP 0.035 0.002 TRP B 183 HIS 0.010 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00456 (13902) covalent geometry : angle 0.64892 (18871) SS BOND : bond 0.00762 ( 2) SS BOND : angle 2.94465 ( 4) hydrogen bonds : bond 0.03529 ( 620) hydrogen bonds : angle 5.45703 ( 1740) *********************** 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 319 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 242 time to evaluate : 0.481 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 152 LYS cc_start: 0.6775 (OUTLIER) cc_final: 0.6283 (mptm) REVERT: A 477 TYR cc_start: 0.8652 (m-80) cc_final: 0.8148 (m-80) REVERT: A 745 TRP cc_start: 0.7641 (p-90) cc_final: 0.7124 (p90) REVERT: A 797 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.6174 (t70) REVERT: A 805 ASN cc_start: 0.9015 (t0) cc_final: 0.8700 (t0) REVERT: B 306 MET cc_start: 0.5926 (mtt) cc_final: 0.5588 (mtt) REVERT: B 345 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.6134 (m-10) REVERT: D 184 TYR cc_start: 0.5751 (m-10) cc_final: 0.5409 (m-10) REVERT: D 188 ARG cc_start: 0.7392 (mmt-90) cc_final: 0.6356 (tpm170) REVERT: D 232 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7304 (pp20) REVERT: D 236 LYS cc_start: 0.8486 (mtpt) cc_final: 0.8254 (ptpt) REVERT: F 1154 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6533 (tp30) REVERT: F 1217 LYS cc_start: 0.5795 (OUTLIER) cc_final: 0.3776 (mtmm) REVERT: F 1224 ARG cc_start: 0.8049 (ptp90) cc_final: 0.7671 (ptp90) REVERT: F 1259 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.5750 (tt) REVERT: F 1279 GLU cc_start: 0.6430 (mp0) cc_final: 0.6167 (mp0) outliers start: 77 outliers final: 63 residues processed: 283 average time/residue: 0.1182 time to fit residues: 48.8589 Evaluate side-chains 294 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 224 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 152 LYS 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 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 514 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 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 157 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 201 THR 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 70 THR Chi-restraints excluded: chain C residue 82 ILE 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 186 THR 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 43 VAL Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 76 VAL 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 1110 SER Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1146 THR Chi-restraints excluded: chain F residue 1154 GLU Chi-restraints excluded: chain F residue 1172 GLU Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1212 LYS Chi-restraints excluded: chain F residue 1217 LYS Chi-restraints excluded: chain F residue 1259 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 168 optimal weight: 0.0980 chunk 1 optimal weight: 30.0000 chunk 85 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 107 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1026 ASN ** 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 = 0.4730 r_free = 0.4730 target = 0.223765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.170849 restraints weight = 16991.612| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 3.22 r_work: 0.4000 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.8572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13904 Z= 0.133 Angle : 0.629 16.923 18875 Z= 0.325 Chirality : 0.045 0.183 2043 Planarity : 0.004 0.050 2482 Dihedral : 5.098 64.298 1909 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.12 % Allowed : 20.61 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.20), residues: 1720 helix: 1.33 (0.28), residues: 328 sheet: -0.38 (0.21), residues: 578 loop : -1.48 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 421 TYR 0.027 0.001 TYR D 79 PHE 0.020 0.001 PHE D 95 TRP 0.023 0.002 TRP B 183 HIS 0.009 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00292 (13902) covalent geometry : angle 0.62793 (18871) SS BOND : bond 0.00603 ( 2) SS BOND : angle 2.74509 ( 4) hydrogen bonds : bond 0.03180 ( 620) hydrogen bonds : angle 5.17002 ( 1740) *********************** 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 322 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 248 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6325 (mptm) REVERT: A 745 TRP cc_start: 0.7593 (p-90) cc_final: 0.7173 (p90) REVERT: A 797 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.5948 (t70) REVERT: A 805 ASN cc_start: 0.9025 (t0) cc_final: 0.8730 (t0) REVERT: B 82 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7313 (mtpt) REVERT: B 215 ARG cc_start: 0.7367 (mtm-85) cc_final: 0.6971 (mtm-85) REVERT: B 306 MET cc_start: 0.5959 (mtt) cc_final: 0.5695 (mtt) REVERT: B 388 TYR cc_start: 0.7916 (m-80) cc_final: 0.7560 (m-80) REVERT: D 188 ARG cc_start: 0.7298 (mmt-90) cc_final: 0.6513 (tpm170) REVERT: D 232 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7429 (pp20) REVERT: F 1168 GLU cc_start: 0.4748 (mp0) cc_final: 0.4531 (mp0) REVERT: F 1172 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.5790 (tt0) REVERT: F 1224 ARG cc_start: 0.8006 (ptp90) cc_final: 0.7652 (ptp90) REVERT: F 1259 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6015 (tt) outliers start: 74 outliers final: 52 residues processed: 289 average time/residue: 0.1229 time to fit residues: 51.8717 Evaluate side-chains 283 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 226 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 430 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 783 LEU 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 157 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 201 THR 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 369 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1146 THR Chi-restraints excluded: chain F residue 1172 GLU Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1259 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 59 optimal weight: 7.9990 chunk 81 optimal weight: 0.0980 chunk 145 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 170 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1036 ASN ** F1086 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 = 0.4713 r_free = 0.4713 target = 0.222654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.166220 restraints weight = 17125.014| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 3.23 r_work: 0.3974 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.8781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13904 Z= 0.158 Angle : 0.642 11.141 18875 Z= 0.336 Chirality : 0.045 0.174 2043 Planarity : 0.004 0.044 2482 Dihedral : 5.110 63.134 1909 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.63 % Allowed : 20.95 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.20), residues: 1720 helix: 1.39 (0.29), residues: 327 sheet: -0.40 (0.21), residues: 574 loop : -1.49 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F1205 TYR 0.029 0.002 TYR B 345 PHE 0.020 0.001 PHE D 95 TRP 0.022 0.002 TRP B 183 HIS 0.012 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00356 (13902) covalent geometry : angle 0.64118 (18871) SS BOND : bond 0.00678 ( 2) SS BOND : angle 2.86226 ( 4) hydrogen bonds : bond 0.03330 ( 620) hydrogen bonds : angle 5.24801 ( 1740) *********************** 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 301 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 234 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6303 (mptm) REVERT: A 294 GLU cc_start: 0.6565 (mp0) cc_final: 0.6304 (mp0) REVERT: A 711 MET cc_start: 0.6293 (ppp) cc_final: 0.6081 (ppp) REVERT: A 741 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6159 (ptm) REVERT: A 745 TRP cc_start: 0.7599 (p-90) cc_final: 0.7133 (p90) REVERT: A 797 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.5836 (t70) REVERT: A 805 ASN cc_start: 0.9010 (t0) cc_final: 0.8733 (t0) REVERT: B 82 LYS cc_start: 0.7838 (mmtt) cc_final: 0.7249 (mtpt) REVERT: B 306 MET cc_start: 0.5988 (mtt) cc_final: 0.5683 (mtt) REVERT: B 388 TYR cc_start: 0.7877 (m-80) cc_final: 0.7673 (m-80) REVERT: D 188 ARG cc_start: 0.7425 (mmt-90) cc_final: 0.6534 (tpm170) REVERT: D 219 GLU cc_start: 0.7526 (tp30) cc_final: 0.7280 (tp30) REVERT: D 232 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7397 (pp20) REVERT: F 1168 GLU cc_start: 0.4791 (mp0) cc_final: 0.4566 (mp0) REVERT: F 1202 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.5628 (tp) REVERT: F 1224 ARG cc_start: 0.8003 (ptp90) cc_final: 0.7655 (ptp90) REVERT: F 1259 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.5798 (tt) outliers start: 67 outliers final: 56 residues processed: 274 average time/residue: 0.1170 time to fit residues: 47.2875 Evaluate side-chains 282 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 220 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 248 THR 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 458 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 581 LEU 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 741 MET Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 783 LEU 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 157 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 201 THR 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 322 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 THR 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 36 ASN Chi-restraints excluded: chain E residue 53 GLN 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 1110 SER Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1146 THR Chi-restraints excluded: chain F residue 1202 LEU 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 66 optimal weight: 0.0030 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 148 optimal weight: 0.0670 chunk 65 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 overall best weight: 0.9932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A 446 GLN ** B 62 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** ** F1086 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 = 0.4732 r_free = 0.4732 target = 0.224533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.166938 restraints weight = 17060.272| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 3.32 r_work: 0.4001 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.8882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13904 Z= 0.133 Angle : 0.627 11.149 18875 Z= 0.327 Chirality : 0.045 0.207 2043 Planarity : 0.004 0.038 2482 Dihedral : 4.992 59.653 1909 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.08 % Allowed : 21.65 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.20), residues: 1720 helix: 1.54 (0.29), residues: 326 sheet: -0.43 (0.20), residues: 590 loop : -1.49 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 421 TYR 0.033 0.001 TYR D 79 PHE 0.019 0.001 PHE D 95 TRP 0.020 0.002 TRP B 183 HIS 0.009 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00296 (13902) covalent geometry : angle 0.62601 (18871) SS BOND : bond 0.00609 ( 2) SS BOND : angle 2.71746 ( 4) hydrogen bonds : bond 0.03169 ( 620) hydrogen bonds : angle 5.11747 ( 1740) ********************** 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 289 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 230 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6374 (mptm) REVERT: A 741 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6221 (ptm) REVERT: A 745 TRP cc_start: 0.7551 (p-90) cc_final: 0.7135 (p90) REVERT: A 805 ASN cc_start: 0.9025 (t0) cc_final: 0.8739 (t0) REVERT: B 82 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7299 (mtpt) REVERT: B 388 TYR cc_start: 0.7850 (m-80) cc_final: 0.7604 (m-10) REVERT: D 32 PRO cc_start: 0.6320 (Cg_endo) cc_final: 0.6054 (Cg_exo) REVERT: D 188 ARG cc_start: 0.7339 (mmt-90) cc_final: 0.6498 (tpm170) REVERT: D 219 GLU cc_start: 0.7512 (tp30) cc_final: 0.7271 (tp30) REVERT: F 1168 GLU cc_start: 0.4718 (mp0) cc_final: 0.4487 (mp0) REVERT: F 1175 TYR cc_start: 0.4819 (t80) cc_final: 0.3409 (t80) REVERT: F 1224 ARG cc_start: 0.7964 (ptp90) cc_final: 0.7627 (ptp90) outliers start: 59 outliers final: 53 residues processed: 263 average time/residue: 0.1176 time to fit residues: 45.3472 Evaluate side-chains 274 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 219 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 430 ILE Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 201 THR 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 322 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1110 SER Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1146 THR Chi-restraints excluded: chain F residue 1202 LEU Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1259 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 147 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 114 optimal weight: 20.0000 chunk 115 optimal weight: 0.0570 chunk 157 optimal weight: 5.9990 chunk 32 optimal weight: 0.0980 overall best weight: 1.8304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN ** F1086 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 = 0.4709 r_free = 0.4709 target = 0.222076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.162867 restraints weight = 17258.353| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 3.44 r_work: 0.3929 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.9046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13904 Z= 0.182 Angle : 0.659 9.617 18875 Z= 0.345 Chirality : 0.046 0.201 2043 Planarity : 0.004 0.039 2482 Dihedral : 5.134 64.956 1909 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.50 % Allowed : 21.78 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.20), residues: 1720 helix: 1.39 (0.28), residues: 326 sheet: -0.46 (0.21), residues: 583 loop : -1.51 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 421 TYR 0.035 0.002 TYR D 79 PHE 0.019 0.002 PHE D 95 TRP 0.026 0.002 TRP B 183 HIS 0.010 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00410 (13902) covalent geometry : angle 0.65747 (18871) SS BOND : bond 0.00783 ( 2) SS BOND : angle 3.03984 ( 4) hydrogen bonds : bond 0.03366 ( 620) hydrogen bonds : angle 5.24578 ( 1740) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4095.66 seconds wall clock time: 72 minutes 31.95 seconds (4351.95 seconds total)