Starting phenix.real_space_refine on Mon Dec 30 14:27:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qn4_18507/12_2024/8qn4_18507.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qn4_18507/12_2024/8qn4_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_18507/12_2024/8qn4_18507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qn4_18507/12_2024/8qn4_18507.map" model { file = "/net/cci-nas-00/data/ceres_data/8qn4_18507/12_2024/8qn4_18507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qn4_18507/12_2024/8qn4_18507.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 8571 2.51 5 N 2324 2.21 5 O 2674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13608 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6231 Classifications: {'peptide': 787} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 757} Chain: "B" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2750 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 355} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 407 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 5, 'TRANS': 50} Chain: "D" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1722 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 645 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "F" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1853 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 233} Chain breaks: 5 Time building chain proxies: 7.59, per 1000 atoms: 0.56 Number of scatterers: 13608 At special positions: 0 Unit cell: (126.48, 123.69, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 2674 8.00 N 2324 7.00 C 8571 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS F1293 " distance=2.04 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.56 Conformation dependent library (CDL) restraints added in 2.1 seconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3172 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 16 sheets defined 19.7% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.829A pdb=" N ILE A 59 " --> pdb=" O ASN A 55 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.686A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN A 113 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 144 removed outlier: 4.043A pdb=" N ASP A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.529A pdb=" N GLY A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.727A pdb=" N VAL A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.293A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 removed outlier: 3.716A pdb=" N ARG A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.502A pdb=" N MET A 552 " --> pdb=" O TYR A 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.547A pdb=" N LEU C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 removed outlier: 3.521A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 62 removed outlier: 3.780A pdb=" N ALA D 57 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 83 removed outlier: 3.587A pdb=" N TYR D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 removed outlier: 3.542A pdb=" N ALA D 90 " --> pdb=" O PRO D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.503A pdb=" N MET D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR D 110 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY D 113 " --> pdb=" O MET D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 154 Processing helix chain 'D' and resid 158 through 186 removed outlier: 4.667A pdb=" N ASP D 162 " --> pdb=" O GLN D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.693A pdb=" N VAL D 195 " --> pdb=" O TRP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.594A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.630A pdb=" N MET D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 240 Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.691A pdb=" N TYR E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 1012 through 1034 removed outlier: 4.122A pdb=" N ASN F1026 " --> pdb=" O VAL F1022 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG F1028 " --> pdb=" O ASN F1024 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N MET F1029 " --> pdb=" O LEU F1025 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 3.558A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.948A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N SER A 100 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 177 through 183 removed outlier: 7.355A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 255 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 removed outlier: 3.957A pdb=" N GLU A 294 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLY A 270 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.718A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP A 399 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 802 through 806 removed outlier: 4.228A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP A 745 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 487 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N TYR A 454 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 448 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA F1266 " --> pdb=" O PHE F1274 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F1282 " --> pdb=" O MET F1258 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU F1202 " --> pdb=" O LEU F1233 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE F1203 " --> pdb=" O VAL F1174 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA F1117 " --> pdb=" O PHE F1113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 673 removed outlier: 6.615A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 50 through 51 removed outlier: 4.041A pdb=" N THR B 50 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 removed outlier: 4.140A pdb=" N ALA B 74 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 202 Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.863A pdb=" N ARG B 281 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 269 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.536A pdb=" N ILE B 290 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP B 292 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.512A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.615A pdb=" N THR E 94 " --> pdb=" O ASN E 103 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1740 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2922 1.34 - 1.46: 4941 1.46 - 1.59: 5965 1.59 - 1.72: 0 1.72 - 1.84: 74 Bond restraints: 13902 Sorted by residual: bond pdb=" CA VAL B 286 " pdb=" C VAL B 286 " ideal model delta sigma weight residual 1.524 1.465 0.060 1.06e-02 8.90e+03 3.17e+01 bond pdb=" CA GLY B 210 " pdb=" C GLY B 210 " ideal model delta sigma weight residual 1.517 1.467 0.050 9.60e-03 1.09e+04 2.72e+01 bond pdb=" CA TYR D 62 " pdb=" CB TYR D 62 " ideal model delta sigma weight residual 1.527 1.576 -0.049 1.05e-02 9.07e+03 2.18e+01 bond pdb=" CA GLY F1211 " pdb=" C GLY F1211 " ideal model delta sigma weight residual 1.513 1.467 0.046 1.08e-02 8.57e+03 1.79e+01 bond pdb=" CA SER A 657 " pdb=" C SER A 657 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.28e-02 6.10e+03 1.74e+01 ... (remaining 13897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 17285 3.61 - 7.21: 1497 7.21 - 10.82: 82 10.82 - 14.42: 5 14.42 - 18.03: 2 Bond angle restraints: 18871 Sorted by residual: angle pdb=" N GLY B 196 " pdb=" CA GLY B 196 " pdb=" C GLY B 196 " ideal model delta sigma weight residual 112.04 94.01 18.03 1.02e+00 9.61e-01 3.12e+02 angle pdb=" C VAL B 286 " pdb=" CA VAL B 286 " pdb=" CB VAL B 286 " ideal model delta sigma weight residual 111.05 102.79 8.26 8.90e-01 1.26e+00 8.61e+01 angle pdb=" CA ASP A 493 " pdb=" CB ASP A 493 " pdb=" CG ASP A 493 " ideal model delta sigma weight residual 112.60 121.22 -8.62 1.00e+00 1.00e+00 7.43e+01 angle pdb=" CA ASN B 287 " pdb=" CB ASN B 287 " pdb=" CG ASN B 287 " ideal model delta sigma weight residual 112.60 104.15 8.45 1.00e+00 1.00e+00 7.14e+01 angle pdb=" N SER D 242 " pdb=" CA SER D 242 " pdb=" C SER D 242 " ideal model delta sigma weight residual 110.80 128.19 -17.39 2.13e+00 2.20e-01 6.66e+01 ... (remaining 18866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.76: 7655 18.76 - 37.51: 367 37.51 - 56.27: 77 56.27 - 75.02: 54 75.02 - 93.78: 28 Dihedral angle restraints: 8181 sinusoidal: 3186 harmonic: 4995 Sorted by residual: dihedral pdb=" CA LYS B 280 " pdb=" C LYS B 280 " pdb=" N ARG B 281 " pdb=" CA ARG B 281 " ideal model delta harmonic sigma weight residual 180.00 135.24 44.76 0 5.00e+00 4.00e-02 8.01e+01 dihedral pdb=" N SER D 243 " pdb=" C SER D 243 " pdb=" CA SER D 243 " pdb=" CB SER D 243 " ideal model delta harmonic sigma weight residual 122.80 140.97 -18.17 0 2.50e+00 1.60e-01 5.28e+01 dihedral pdb=" N SER D 242 " pdb=" C SER D 242 " pdb=" CA SER D 242 " pdb=" CB SER D 242 " ideal model delta harmonic sigma weight residual 122.80 139.91 -17.11 0 2.50e+00 1.60e-01 4.68e+01 ... (remaining 8178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 1705 0.158 - 0.317: 308 0.317 - 0.475: 25 0.475 - 0.634: 4 0.634 - 0.792: 1 Chirality restraints: 2043 Sorted by residual: chirality pdb=" CA SER D 242 " pdb=" N SER D 242 " pdb=" C SER D 242 " pdb=" CB SER D 242 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" CA ARG F1269 " pdb=" N ARG F1269 " pdb=" C ARG F1269 " pdb=" CB ARG F1269 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" CA SER D 243 " pdb=" N SER D 243 " pdb=" C SER D 243 " pdb=" CB SER D 243 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.02e+00 ... (remaining 2040 not shown) Planarity restraints: 2482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 686 " 0.151 2.00e-02 2.50e+03 1.22e-01 2.99e+02 pdb=" CG TYR A 686 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 686 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR A 686 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 TYR A 686 " -0.155 2.00e-02 2.50e+03 pdb=" CE2 TYR A 686 " -0.093 2.00e-02 2.50e+03 pdb=" CZ TYR A 686 " -0.045 2.00e-02 2.50e+03 pdb=" OH TYR A 686 " 0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 255 " -0.216 2.00e-02 2.50e+03 1.12e-01 2.53e+02 pdb=" CG TYR A 255 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR A 255 " 0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR A 255 " 0.124 2.00e-02 2.50e+03 pdb=" CE1 TYR A 255 " 0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR A 255 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 255 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 255 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F1274 " -0.132 2.00e-02 2.50e+03 1.02e-01 1.83e+02 pdb=" CG PHE F1274 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE F1274 " 0.183 2.00e-02 2.50e+03 pdb=" CD2 PHE F1274 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE F1274 " -0.084 2.00e-02 2.50e+03 pdb=" CE2 PHE F1274 " 0.043 2.00e-02 2.50e+03 pdb=" CZ PHE F1274 " -0.097 2.00e-02 2.50e+03 ... (remaining 2479 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1240 2.75 - 3.29: 12249 3.29 - 3.82: 21911 3.82 - 4.36: 27852 4.36 - 4.90: 46384 Nonbonded interactions: 109636 Sorted by model distance: nonbonded pdb=" N GLY B 196 " pdb=" O GLY B 196 " model vdw 2.210 2.496 nonbonded pdb=" N THR F1162 " pdb=" O THR F1162 " model vdw 2.405 2.496 nonbonded pdb=" N TYR A 432 " pdb=" O TYR A 432 " model vdw 2.438 2.496 nonbonded pdb=" N SER B 126 " pdb=" O SER B 126 " model vdw 2.453 2.496 nonbonded pdb=" N GLY A 638 " pdb=" O GLY A 638 " model vdw 2.461 2.496 ... (remaining 109631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.590 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.490 ------------------------------------------------------------------------------- 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 13902 Z= 1.095 Angle : 2.080 18.029 18871 Z= 1.401 Chirality : 0.121 0.792 2043 Planarity : 0.019 0.220 2482 Dihedral : 14.779 93.777 5003 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.64 % Favored : 94.24 % Rotamer: Outliers : 0.76 % Allowed : 5.53 % Favored : 93.71 % Cbeta Deviations : 0.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.18), residues: 1720 helix: -0.33 (0.28), residues: 316 sheet: -0.36 (0.21), residues: 548 loop : -2.43 (0.17), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.167 0.024 TRP B 183 HIS 0.025 0.006 HIS B 324 PHE 0.183 0.020 PHE F1274 TYR 0.230 0.030 TYR A 686 ARG 0.057 0.004 ARG F1224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 504 time to evaluate : 1.574 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: 0.3278 time to fit residues: 235.0012 Evaluate side-chains 289 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 284 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 155 optimal weight: 30.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 102 ASN A 170 GLN A 215 GLN ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN A 411 GLN A 563 ASN A 748 ASN A 803 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 350 ASN D 54 GLN D 60 ASN ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 54 GLN E 71 ASN F1023 ASN F1024 ASN F1064 GLN ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5003 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 13902 Z= 0.241 Angle : 0.697 9.190 18871 Z= 0.376 Chirality : 0.048 0.161 2043 Planarity : 0.005 0.041 2482 Dihedral : 6.168 76.185 1921 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.50 % Allowed : 11.96 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.18), residues: 1720 helix: 0.44 (0.27), residues: 328 sheet: -0.21 (0.20), residues: 580 loop : -1.99 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 93 HIS 0.013 0.002 HIS D 102 PHE 0.031 0.002 PHE A 565 TYR 0.038 0.002 TYR D 79 ARG 0.009 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 301 time to evaluate : 1.560 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 outliers start: 65 outliers final: 33 residues processed: 341 average time/residue: 0.2994 time to fit residues: 145.5084 Evaluate side-chains 275 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 242 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 0.0570 chunk 48 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 155 optimal weight: 30.0000 chunk 168 optimal weight: 0.0870 chunk 138 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 overall best weight: 2.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN A 533 HIS B 85 ASN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 350 ASN B 368 GLN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN E 54 GLN E 80 GLN E 89 GLN F1130 ASN F1160 HIS ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5332 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 13902 Z= 0.296 Angle : 0.698 9.461 18871 Z= 0.375 Chirality : 0.047 0.167 2043 Planarity : 0.005 0.050 2482 Dihedral : 5.832 77.272 1912 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.29 % Allowed : 15.98 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.19), residues: 1720 helix: 0.65 (0.28), residues: 337 sheet: -0.23 (0.20), residues: 588 loop : -1.72 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 546 HIS 0.009 0.002 HIS D 102 PHE 0.025 0.002 PHE A 478 TYR 0.043 0.002 TYR D 79 ARG 0.008 0.001 ARG F1205 *********************** 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 326 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 264 time to evaluate : 1.494 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 578 TYR cc_start: 0.6473 (t80) cc_final: 0.5766 (t80) REVERT: A 646 MET cc_start: 0.6994 (tpp) cc_final: 0.6607 (tpt) REVERT: A 797 ASP cc_start: 0.4166 (OUTLIER) cc_final: 0.3963 (t0) REVERT: B 163 LEU cc_start: 0.7508 (mp) cc_final: 0.7213 (mt) REVERT: B 197 GLU cc_start: 0.6073 (OUTLIER) cc_final: 0.5697 (mt-10) outliers start: 62 outliers final: 45 residues processed: 302 average time/residue: 0.2777 time to fit residues: 121.3063 Evaluate side-chains 264 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 217 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 357 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 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 E residue 53 GLN Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1085 THR Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1128 HIS Chi-restraints excluded: chain F residue 1130 ASN Chi-restraints excluded: chain F residue 1210 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 20.0000 chunk 116 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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** A 448 ASN A 466 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 334 ASN B 336 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN ** F1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1130 ASN ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1230 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5663 moved from start: 0.7813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.140 13902 Z= 0.540 Angle : 0.829 8.737 18871 Z= 0.447 Chirality : 0.052 0.292 2043 Planarity : 0.006 0.045 2482 Dihedral : 6.347 72.794 1911 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 6.36 % Allowed : 16.46 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.19), residues: 1720 helix: -0.00 (0.27), residues: 337 sheet: -0.55 (0.21), residues: 575 loop : -2.01 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 739 HIS 0.012 0.002 HIS B 121 PHE 0.026 0.003 PHE D 95 TYR 0.040 0.003 TYR D 79 ARG 0.005 0.001 ARG B 281 *********************** 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 340 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 248 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.5640 (m-80) REVERT: A 646 MET cc_start: 0.7579 (tpp) cc_final: 0.6998 (tpt) REVERT: A 797 ASP cc_start: 0.5164 (OUTLIER) cc_final: 0.4643 (t0) REVERT: B 163 LEU cc_start: 0.7714 (mp) cc_final: 0.7507 (mt) REVERT: F 1217 LYS cc_start: 0.5658 (OUTLIER) cc_final: 0.4171 (mtmm) REVERT: F 1258 MET cc_start: 0.4777 (mmm) cc_final: 0.4535 (mmp) outliers start: 92 outliers final: 63 residues processed: 310 average time/residue: 0.2579 time to fit residues: 118.5449 Evaluate side-chains 285 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 219 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 458 ILE 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 571 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 768 MET 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 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 281 ARG 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 328 THR 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 60 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 195 VAL Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain E residue 48 VAL 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 1128 HIS Chi-restraints excluded: chain F residue 1172 GLU Chi-restraints excluded: chain F residue 1210 VAL 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 137 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 84 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS B 350 ASN B 368 GLN E 36 ASN E 54 GLN F1023 ASN F1026 ASN ** F1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1130 ASN ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5470 moved from start: 0.7887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13902 Z= 0.189 Angle : 0.622 8.966 18871 Z= 0.329 Chirality : 0.045 0.196 2043 Planarity : 0.004 0.039 2482 Dihedral : 5.390 69.126 1909 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.73 % Allowed : 22.20 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.19), residues: 1720 helix: 0.86 (0.28), residues: 329 sheet: -0.40 (0.20), residues: 601 loop : -1.67 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 546 HIS 0.012 0.001 HIS D 102 PHE 0.036 0.002 PHE A 802 TYR 0.036 0.001 TYR D 79 ARG 0.005 0.001 ARG D 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 251 time to evaluate : 1.589 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: 0.4674 (OUTLIER) cc_final: 0.4167 (mptm) REVERT: A 646 MET cc_start: 0.7348 (tpp) cc_final: 0.6930 (tpt) REVERT: A 797 ASP cc_start: 0.4759 (OUTLIER) cc_final: 0.4373 (t0) REVERT: B 163 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7204 (mt) REVERT: F 1290 ASN cc_start: 0.4815 (p0) cc_final: 0.4563 (p0) outliers start: 54 outliers final: 37 residues processed: 280 average time/residue: 0.2956 time to fit residues: 123.4948 Evaluate side-chains 253 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 1.541 ------------------------------------------------------------------------------- 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 181 ASN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 550 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 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 126 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 303 ASP 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 D residue 48 TRP Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1128 HIS Chi-restraints excluded: chain F residue 1130 ASN Chi-restraints excluded: chain F residue 1210 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN ** F1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5664 moved from start: 0.8506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 13902 Z= 0.400 Angle : 0.724 11.161 18871 Z= 0.385 Chirality : 0.048 0.187 2043 Planarity : 0.005 0.065 2482 Dihedral : 5.827 79.852 1909 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 5.19 % Allowed : 19.85 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.19), residues: 1720 helix: 0.38 (0.28), residues: 338 sheet: -0.60 (0.20), residues: 590 loop : -1.79 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 183 HIS 0.014 0.002 HIS D 102 PHE 0.026 0.002 PHE A 440 TYR 0.039 0.002 TYR D 79 ARG 0.012 0.001 ARG A 421 *********************** 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 306 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 231 time to evaluate : 1.515 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: 0.4886 (OUTLIER) cc_final: 0.4359 (mptm) REVERT: A 368 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6850 (mm-30) REVERT: A 646 MET cc_start: 0.7707 (tpp) cc_final: 0.7079 (tpt) REVERT: A 777 MET cc_start: 0.5184 (tpp) cc_final: 0.4884 (tpt) REVERT: A 797 ASP cc_start: 0.5114 (OUTLIER) cc_final: 0.4639 (t70) REVERT: B 163 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7295 (mt) REVERT: F 1217 LYS cc_start: 0.5471 (OUTLIER) cc_final: 0.3573 (mtmm) REVERT: F 1290 ASN cc_start: 0.4835 (p0) cc_final: 0.4483 (p0) outliers start: 75 outliers final: 58 residues processed: 278 average time/residue: 0.2544 time to fit residues: 104.6463 Evaluate side-chains 278 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 216 time to evaluate : 1.571 ------------------------------------------------------------------------------- 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 181 ASN 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 473 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 69 VAL 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 E residue 43 VAL Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1085 THR Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1210 VAL Chi-restraints excluded: chain F residue 1217 LYS Chi-restraints excluded: chain F residue 1224 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 30.0000 chunk 18 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5634 moved from start: 0.8744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 13902 Z= 0.311 Angle : 0.672 9.930 18871 Z= 0.357 Chirality : 0.047 0.145 2043 Planarity : 0.004 0.038 2482 Dihedral : 5.566 69.919 1909 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.84 % Allowed : 21.23 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.20), residues: 1720 helix: 0.70 (0.28), residues: 330 sheet: -0.58 (0.20), residues: 591 loop : -1.72 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 183 HIS 0.012 0.001 HIS D 102 PHE 0.026 0.002 PHE A 440 TYR 0.032 0.002 TYR D 79 ARG 0.011 0.001 ARG A 421 *********************** 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 308 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 238 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.4896 (OUTLIER) cc_final: 0.4393 (mptm) REVERT: A 646 MET cc_start: 0.7528 (tpp) cc_final: 0.7010 (tpt) REVERT: A 777 MET cc_start: 0.5044 (tpp) cc_final: 0.4813 (tpt) REVERT: B 163 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7233 (mt) REVERT: F 1290 ASN cc_start: 0.4997 (p0) cc_final: 0.4635 (p0) outliers start: 70 outliers final: 54 residues processed: 283 average time/residue: 0.2622 time to fit residues: 109.3145 Evaluate side-chains 278 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 222 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 181 ASN Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 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 786 SER 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 126 SER Chi-restraints excluded: chain B residue 163 LEU 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 327 LEU Chi-restraints excluded: chain B residue 337 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 E residue 43 VAL Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1085 THR Chi-restraints excluded: chain F residue 1210 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 112 optimal weight: 0.2980 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** ** A 709 ASN ** 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 213 ASN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 350 ASN B 368 GLN D 230 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5505 moved from start: 0.8800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13902 Z= 0.177 Angle : 0.625 9.670 18871 Z= 0.327 Chirality : 0.045 0.144 2043 Planarity : 0.004 0.083 2482 Dihedral : 5.155 59.606 1909 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.67 % Allowed : 22.54 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1720 helix: 1.16 (0.29), residues: 332 sheet: -0.37 (0.21), residues: 582 loop : -1.59 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 317 HIS 0.007 0.001 HIS D 102 PHE 0.027 0.001 PHE A 440 TYR 0.028 0.001 TYR B 345 ARG 0.012 0.000 ARG A 421 *********************** 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 302 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 249 time to evaluate : 1.515 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: 0.4716 (OUTLIER) cc_final: 0.4152 (mptm) REVERT: A 646 MET cc_start: 0.7444 (tpp) cc_final: 0.6979 (tpt) REVERT: A 797 ASP cc_start: 0.5039 (OUTLIER) cc_final: 0.4662 (t70) REVERT: B 163 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7139 (mt) REVERT: F 1290 ASN cc_start: 0.5128 (p0) cc_final: 0.4712 (p0) outliers start: 53 outliers final: 39 residues processed: 279 average time/residue: 0.2722 time to fit residues: 110.3208 Evaluate side-chains 269 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 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 532 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 205 TYR 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 1210 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 66 optimal weight: 0.0870 chunk 120 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 B 165 HIS ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5493 moved from start: 0.8876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13902 Z= 0.181 Angle : 0.630 9.494 18871 Z= 0.328 Chirality : 0.045 0.151 2043 Planarity : 0.004 0.059 2482 Dihedral : 4.972 56.476 1909 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.25 % Allowed : 23.51 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.20), residues: 1720 helix: 1.33 (0.29), residues: 332 sheet: -0.35 (0.21), residues: 593 loop : -1.55 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 317 HIS 0.005 0.001 HIS D 102 PHE 0.027 0.001 PHE A 440 TYR 0.028 0.001 TYR D 79 ARG 0.013 0.000 ARG A 421 *********************** 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 274 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 227 time to evaluate : 1.667 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: 0.4772 (OUTLIER) cc_final: 0.4016 (mptm) REVERT: A 646 MET cc_start: 0.7377 (tpp) cc_final: 0.6964 (tpt) REVERT: A 797 ASP cc_start: 0.5177 (OUTLIER) cc_final: 0.4691 (t70) REVERT: B 163 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7099 (mt) REVERT: D 32 PRO cc_start: 0.4619 (Cg_endo) cc_final: 0.4364 (Cg_exo) outliers start: 47 outliers final: 39 residues processed: 253 average time/residue: 0.2637 time to fit residues: 98.6261 Evaluate side-chains 262 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 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 797 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR 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 1210 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 30.0000 chunk 99 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 135 optimal weight: 0.1980 chunk 14 optimal weight: 30.0000 chunk 104 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1024 ASN F1036 ASN ** F1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5720 moved from start: 0.9407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 13902 Z= 0.431 Angle : 0.779 9.891 18871 Z= 0.412 Chirality : 0.050 0.306 2043 Planarity : 0.005 0.069 2482 Dihedral : 5.781 73.571 1909 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.73 % Allowed : 23.65 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1720 helix: 0.68 (0.29), residues: 327 sheet: -0.62 (0.21), residues: 571 loop : -1.64 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP B 317 HIS 0.011 0.002 HIS D 102 PHE 0.025 0.002 PHE A 440 TYR 0.035 0.002 TYR D 79 ARG 0.013 0.001 ARG A 421 ********************** 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 274 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.4954 (OUTLIER) cc_final: 0.4439 (mptm) REVERT: A 578 TYR cc_start: 0.6530 (t80) cc_final: 0.5741 (t80) REVERT: A 646 MET cc_start: 0.7570 (tpp) cc_final: 0.7045 (tpt) REVERT: A 797 ASP cc_start: 0.5665 (OUTLIER) cc_final: 0.4882 (t70) REVERT: D 32 PRO cc_start: 0.4876 (Cg_endo) cc_final: 0.4670 (Cg_exo) REVERT: F 1260 MET cc_start: 0.6901 (tmm) cc_final: 0.6691 (tmm) outliers start: 54 outliers final: 41 residues processed: 255 average time/residue: 0.2798 time to fit residues: 103.3645 Evaluate side-chains 252 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 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 611 VAL Chi-restraints excluded: chain A residue 612 THR 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 768 MET Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 311 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 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 52 ILE Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 145 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 F residue 1065 VAL Chi-restraints excluded: chain F residue 1127 HIS Chi-restraints excluded: chain F residue 1210 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 135 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4695 r_free = 0.4695 target = 0.225406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.167812 restraints weight = 17024.324| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 3.33 r_work: 0.3987 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.9382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13902 Z= 0.202 Angle : 0.681 11.511 18871 Z= 0.352 Chirality : 0.046 0.198 2043 Planarity : 0.004 0.071 2482 Dihedral : 5.239 61.747 1909 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.56 % Allowed : 24.97 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.20), residues: 1720 helix: 1.08 (0.28), residues: 333 sheet: -0.45 (0.21), residues: 586 loop : -1.63 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 317 HIS 0.007 0.001 HIS D 102 PHE 0.022 0.001 PHE A 440 TYR 0.025 0.001 TYR D 79 ARG 0.014 0.001 ARG A 421 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3343.83 seconds wall clock time: 62 minutes 27.00 seconds (3747.00 seconds total)