Starting phenix.real_space_refine on Wed Apr 10 09:31:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx7_40826/04_2024/8sx7_40826_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx7_40826/04_2024/8sx7_40826.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx7_40826/04_2024/8sx7_40826_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx7_40826/04_2024/8sx7_40826_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx7_40826/04_2024/8sx7_40826_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx7_40826/04_2024/8sx7_40826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx7_40826/04_2024/8sx7_40826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx7_40826/04_2024/8sx7_40826_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx7_40826/04_2024/8sx7_40826_trim_updated.pdb" } resolution = 2.7 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= 0.002 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 38 5.16 5 C 6177 2.51 5 N 1602 2.21 5 O 1701 1.98 5 H 9719 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19237 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 19203 Classifications: {'peptide': 1188} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 1151} Chain breaks: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {'ZWY': 1} Classifications: {'undetermined': 1, 'water': 3} Link IDs: {None: 3} Time building chain proxies: 8.74, per 1000 atoms: 0.45 Number of scatterers: 19237 At special positions: 0 Unit cell: (84.335, 94.355, 144.455, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 O 1701 8.00 N 1602 7.00 C 6177 6.00 H 9719 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 15.33 Conformation dependent library (CDL) restraints added in 1.8 seconds 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2246 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 4 sheets defined 65.2% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 25 through 36 Proline residue: A 29 - end of helix removed outlier: 3.540A pdb=" N ILE A 33 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 73 removed outlier: 3.807A pdb=" N GLU A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 5.848A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 121 removed outlier: 3.523A pdb=" N GLU A 102 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 103 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN A 109 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.651A pdb=" N LEU A 113 " --> pdb=" O PRO A 110 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 117 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 178 Processing helix chain 'A' and resid 185 through 188 No H-bonds generated for 'chain 'A' and resid 185 through 188' Processing helix chain 'A' and resid 191 through 200 removed outlier: 3.637A pdb=" N LEU A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 210 removed outlier: 3.836A pdb=" N ASP A 206 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 208 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR A 209 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 232 removed outlier: 3.929A pdb=" N TRP A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 217 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLY A 218 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 3.550A pdb=" N VAL A 225 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 229 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 281 removed outlier: 3.509A pdb=" N VAL A 243 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A 248 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.533A pdb=" N PHE A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 262 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 265 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 266 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 269 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 276 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 291 through 325 removed outlier: 3.633A pdb=" N PHE A 295 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 296 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 299 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 303 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 348 through 366 Processing helix chain 'A' and resid 368 through 390 Processing helix chain 'A' and resid 451 through 459 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 537 through 551 removed outlier: 3.592A pdb=" N ALA A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 576 Processing helix chain 'A' and resid 594 through 596 No H-bonds generated for 'chain 'A' and resid 594 through 596' Processing helix chain 'A' and resid 698 through 708 removed outlier: 3.767A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 744 Processing helix chain 'A' and resid 761 through 807 removed outlier: 3.741A pdb=" N PHE A 787 " --> pdb=" O SER A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 814 Processing helix chain 'A' and resid 818 through 833 removed outlier: 3.784A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE A 829 " --> pdb=" O PHE A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 860 Processing helix chain 'A' and resid 862 through 909 Proline residue: A 867 - end of helix Proline residue: A 870 - end of helix removed outlier: 4.011A pdb=" N GLU A 884 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG A 887 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 890 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 893 " --> pdb=" O LYS A 890 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 895 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER A 898 " --> pdb=" O THR A 895 " (cutoff:3.500A) Proline residue: A 899 - end of helix Processing helix chain 'A' and resid 911 through 916 Processing helix chain 'A' and resid 920 through 969 Processing helix chain 'A' and resid 971 through 973 No H-bonds generated for 'chain 'A' and resid 971 through 973' Processing helix chain 'A' and resid 976 through 1017 removed outlier: 4.064A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1088 removed outlier: 3.535A pdb=" N ILE A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1110 through 1114 Processing helix chain 'A' and resid 1143 through 1152 Processing helix chain 'A' and resid 1156 through 1161 Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1179 through 1192 Processing helix chain 'A' and resid 1209 through 1222 removed outlier: 4.309A pdb=" N LEU A1214 " --> pdb=" O ARG A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1237 No H-bonds generated for 'chain 'A' and resid 1235 through 1237' Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'A' and resid 1268 through 1276 removed outlier: 3.631A pdb=" N LEU A1276 " --> pdb=" O MET A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1297 Processing sheet with id= A, first strand: chain 'A' and resid 433 through 435 Processing sheet with id= B, first strand: chain 'A' and resid 610 through 614 removed outlier: 6.890A pdb=" N ILE A 605 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS A 614 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE A 603 " --> pdb=" O LYS A 614 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG A 587 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL A 443 " --> pdb=" O ARG A 587 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 589 " --> pdb=" O VAL A 443 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1063 through 1065 Processing sheet with id= D, first strand: chain 'A' and resid 1252 through 1256 removed outlier: 6.840A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL A1228 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE A1073 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N THR A1230 " --> pdb=" O ILE A1073 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLY A1075 " --> pdb=" O THR A1230 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.29 Time building geometry restraints manager: 16.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9705 1.03 - 1.23: 24 1.23 - 1.42: 4023 1.42 - 1.62: 5629 1.62 - 1.81: 60 Bond restraints: 19441 Sorted by residual: bond pdb=" C15 ZWY A1401 " pdb=" C16 ZWY A1401 " ideal model delta sigma weight residual 0.007 1.506 -1.499 2.00e-02 2.50e+03 5.62e+03 bond pdb=" C18 ZWY A1401 " pdb=" C19 ZWY A1401 " ideal model delta sigma weight residual 0.565 1.456 -0.891 2.00e-02 2.50e+03 1.99e+03 bond pdb=" C05 ZWY A1401 " pdb=" C06 ZWY A1401 " ideal model delta sigma weight residual 0.767 1.517 -0.750 2.00e-02 2.50e+03 1.41e+03 bond pdb=" C16 ZWY A1401 " pdb=" C17 ZWY A1401 " ideal model delta sigma weight residual 2.105 1.453 0.652 2.00e-02 2.50e+03 1.06e+03 bond pdb=" C14 ZWY A1401 " pdb=" C15 ZWY A1401 " ideal model delta sigma weight residual 2.172 1.543 0.629 2.00e-02 2.50e+03 9.90e+02 ... (remaining 19436 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.63: 287 106.63 - 113.54: 23141 113.54 - 120.45: 6604 120.45 - 127.36: 5052 127.36 - 134.26: 113 Bond angle restraints: 35197 Sorted by residual: angle pdb=" C13 ZWY A1401 " pdb=" C14 ZWY A1401 " pdb=" C19 ZWY A1401 " ideal model delta sigma weight residual 169.18 123.67 45.51 3.00e+00 1.11e-01 2.30e+02 angle pdb=" C13 ZWY A1401 " pdb=" C14 ZWY A1401 " pdb=" C15 ZWY A1401 " ideal model delta sigma weight residual 80.34 121.36 -41.02 3.00e+00 1.11e-01 1.87e+02 angle pdb=" C14 ZWY A1401 " pdb=" C15 ZWY A1401 " pdb=" C25 ZWY A1401 " ideal model delta sigma weight residual 70.53 109.77 -39.24 3.00e+00 1.11e-01 1.71e+02 angle pdb=" C05 ZWY A1401 " pdb=" C15 ZWY A1401 " pdb=" C25 ZWY A1401 " ideal model delta sigma weight residual 74.41 109.84 -35.43 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C16 ZWY A1401 " pdb=" C15 ZWY A1401 " pdb=" C25 ZWY A1401 " ideal model delta sigma weight residual 76.63 107.96 -31.33 3.00e+00 1.11e-01 1.09e+02 ... (remaining 35192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.95: 8446 19.95 - 39.91: 327 39.91 - 59.86: 203 59.86 - 79.81: 78 79.81 - 99.76: 4 Dihedral angle restraints: 9058 sinusoidal: 4912 harmonic: 4146 Sorted by residual: dihedral pdb=" CA ASP A 43 " pdb=" C ASP A 43 " pdb=" N MET A 44 " pdb=" CA MET A 44 " ideal model delta harmonic sigma weight residual 180.00 -153.76 -26.24 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA LYS A 585 " pdb=" C LYS A 585 " pdb=" N ILE A 586 " pdb=" CA ILE A 586 " ideal model delta harmonic sigma weight residual 180.00 154.73 25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ALA A1232 " pdb=" C ALA A1232 " pdb=" N HIS A1233 " pdb=" CA HIS A1233 " ideal model delta harmonic sigma weight residual 180.00 156.50 23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 9055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.762: 1519 0.762 - 1.524: 3 1.524 - 2.286: 0 2.286 - 3.047: 1 3.047 - 3.809: 1 Chirality restraints: 1524 Sorted by residual: chirality pdb=" C06 ZWY A1401 " pdb=" C05 ZWY A1401 " pdb=" C07 ZWY A1401 " pdb=" C12 ZWY A1401 " both_signs ideal model delta sigma weight residual False -1.73 2.08 -3.81 2.00e-01 2.50e+01 3.63e+02 chirality pdb=" C15 ZWY A1401 " pdb=" C05 ZWY A1401 " pdb=" C14 ZWY A1401 " pdb=" C16 ZWY A1401 " both_signs ideal model delta sigma weight residual False -0.02 2.74 -2.76 2.00e-01 2.50e+01 1.90e+02 chirality pdb=" C18 ZWY A1401 " pdb=" C17 ZWY A1401 " pdb=" C19 ZWY A1401 " pdb=" O20 ZWY A1401 " both_signs ideal model delta sigma weight residual False -0.77 -1.92 1.15 2.00e-01 2.50e+01 3.33e+01 ... (remaining 1521 not shown) Planarity restraints: 2787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 587 " 0.270 9.50e-02 1.11e+02 9.99e-02 5.08e+01 pdb=" NE ARG A 587 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG A 587 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 587 " 0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG A 587 " -0.085 2.00e-02 2.50e+03 pdb="HH11 ARG A 587 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 587 " -0.040 2.00e-02 2.50e+03 pdb="HH21 ARG A 587 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 587 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 52 " -0.184 9.50e-02 1.11e+02 6.76e-02 2.23e+01 pdb=" NE ARG A 52 " -0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 52 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 52 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 52 " 0.054 2.00e-02 2.50e+03 pdb="HH11 ARG A 52 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 52 " 0.028 2.00e-02 2.50e+03 pdb="HH21 ARG A 52 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 52 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 167 " -0.141 9.50e-02 1.11e+02 5.13e-02 1.15e+01 pdb=" NE ARG A 167 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 167 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 167 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 167 " 0.042 2.00e-02 2.50e+03 pdb="HH11 ARG A 167 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 167 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 167 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 167 " -0.041 2.00e-02 2.50e+03 ... (remaining 2784 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 511 2.11 - 2.73: 33919 2.73 - 3.35: 57138 3.35 - 3.98: 70741 3.98 - 4.60: 113508 Nonbonded interactions: 275817 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 177 " pdb=" OE1 GLU A 394 " model vdw 1.483 1.850 nonbonded pdb=" O LEU A 367 " pdb=" HG SER A 371 " model vdw 1.535 1.850 nonbonded pdb=" O PHE A 333 " pdb=" HG1 THR A 337 " model vdw 1.551 1.850 nonbonded pdb=" O ALA A 296 " pdb=" HG1 THR A 300 " model vdw 1.571 1.850 nonbonded pdb=" OD1 ASP A 842 " pdb=" H1 HOH A1501 " model vdw 1.590 1.850 ... (remaining 275812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.300 Extract box with map and model: 6.610 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 64.920 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 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 : 0.026 1.499 9722 Z= 1.752 Angle : 1.092 45.508 13184 Z= 0.482 Chirality : 0.138 3.809 1524 Planarity : 0.006 0.088 1639 Dihedral : 12.641 99.763 3555 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.39 % Allowed : 2.81 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.48 (0.21), residues: 1180 helix: -1.18 (0.16), residues: 764 sheet: 0.39 (0.63), residues: 51 loop : -0.26 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 734 HIS 0.020 0.002 HIS A 153 PHE 0.022 0.002 PHE A 156 TYR 0.025 0.003 TYR A 123 ARG 0.016 0.002 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 211 time to evaluate : 1.451 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: A 312 ARG cc_start: 0.6690 (mtt-85) cc_final: 0.6363 (mmp80) REVERT: A 1045 ASN cc_start: 0.7853 (t0) cc_final: 0.7286 (t0) outliers start: 4 outliers final: 3 residues processed: 215 average time/residue: 2.1383 time to fit residues: 502.0345 Evaluate side-chains 110 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 1248 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 200 ASN A 725 GLN A 909 GLN A1111 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.168 9722 Z= 0.428 Angle : 0.832 21.452 13184 Z= 0.445 Chirality : 0.064 1.339 1524 Planarity : 0.008 0.054 1639 Dihedral : 7.706 118.745 1311 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.32 % Allowed : 12.20 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.99 (0.22), residues: 1180 helix: -0.79 (0.16), residues: 758 sheet: 0.34 (0.60), residues: 55 loop : -0.07 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 483 HIS 0.008 0.002 HIS A 153 PHE 0.024 0.002 PHE A 352 TYR 0.020 0.002 TYR A 881 ARG 0.010 0.001 ARG A1251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 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: A 121 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5682 (tm-30) REVERT: A 312 ARG cc_start: 0.6866 (mtt-85) cc_final: 0.6533 (mmp80) REVERT: A 319 MET cc_start: 0.7367 (mmm) cc_final: 0.7052 (mmt) REVERT: A 1045 ASN cc_start: 0.7881 (t0) cc_final: 0.7299 (t0) REVERT: A 1113 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7439 (tt) REVERT: A 1166 MET cc_start: 0.5707 (OUTLIER) cc_final: 0.4932 (pmm) outliers start: 24 outliers final: 11 residues processed: 127 average time/residue: 1.7458 time to fit residues: 247.8218 Evaluate side-chains 112 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1204 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.168 9722 Z= 0.428 Angle : 0.832 21.449 13184 Z= 0.445 Chirality : 0.064 1.339 1524 Planarity : 0.008 0.054 1639 Dihedral : 7.683 118.742 1308 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.36 % Allowed : 14.52 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.99 (0.22), residues: 1180 helix: -0.79 (0.16), residues: 758 sheet: 0.34 (0.60), residues: 55 loop : -0.07 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 483 HIS 0.008 0.002 HIS A 153 PHE 0.024 0.002 PHE A 352 TYR 0.020 0.002 TYR A 881 ARG 0.010 0.001 ARG A1251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.202 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 121 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5682 (tm-30) REVERT: A 312 ARG cc_start: 0.6863 (mtt-85) cc_final: 0.6534 (mmp80) REVERT: A 319 MET cc_start: 0.7368 (mmm) cc_final: 0.7050 (mmt) REVERT: A 1045 ASN cc_start: 0.7881 (t0) cc_final: 0.7300 (t0) REVERT: A 1113 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7439 (tt) REVERT: A 1166 MET cc_start: 0.5703 (OUTLIER) cc_final: 0.4931 (pmm) outliers start: 14 outliers final: 11 residues processed: 109 average time/residue: 1.1482 time to fit residues: 141.7284 Evaluate side-chains 108 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1204 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 11 optimal weight: 0.4980 chunk 51 optimal weight: 9.9990 chunk 72 optimal weight: 0.2980 chunk 107 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** A 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.168 9722 Z= 0.427 Angle : 0.832 21.405 13184 Z= 0.445 Chirality : 0.064 1.339 1524 Planarity : 0.008 0.054 1639 Dihedral : 7.659 118.700 1308 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.45 % Allowed : 14.71 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.99 (0.22), residues: 1180 helix: -0.79 (0.16), residues: 758 sheet: 0.34 (0.60), residues: 55 loop : -0.07 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 483 HIS 0.008 0.002 HIS A 153 PHE 0.024 0.002 PHE A 352 TYR 0.020 0.002 TYR A 881 ARG 0.010 0.001 ARG A1251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.421 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 121 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5682 (tm-30) REVERT: A 312 ARG cc_start: 0.6864 (mtt-85) cc_final: 0.6533 (mmp80) REVERT: A 319 MET cc_start: 0.7366 (mmm) cc_final: 0.7049 (mmt) REVERT: A 1045 ASN cc_start: 0.7882 (t0) cc_final: 0.7301 (t0) REVERT: A 1113 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7439 (tt) REVERT: A 1166 MET cc_start: 0.5703 (OUTLIER) cc_final: 0.4931 (pmm) outliers start: 15 outliers final: 12 residues processed: 105 average time/residue: 1.5581 time to fit residues: 185.6016 Evaluate side-chains 108 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1204 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.168 9722 Z= 0.425 Angle : 0.832 20.939 13184 Z= 0.444 Chirality : 0.064 1.338 1524 Planarity : 0.008 0.054 1639 Dihedral : 7.767 118.273 1308 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.36 % Allowed : 14.91 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.99 (0.22), residues: 1180 helix: -0.79 (0.16), residues: 758 sheet: 0.34 (0.60), residues: 55 loop : -0.07 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 483 HIS 0.008 0.002 HIS A 153 PHE 0.024 0.002 PHE A 352 TYR 0.020 0.002 TYR A 881 ARG 0.010 0.001 ARG A1251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.544 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 121 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5681 (tm-30) REVERT: A 312 ARG cc_start: 0.6865 (mtt-85) cc_final: 0.6533 (mmp80) REVERT: A 319 MET cc_start: 0.7365 (mmm) cc_final: 0.7040 (mmt) REVERT: A 1045 ASN cc_start: 0.7883 (t0) cc_final: 0.7301 (t0) REVERT: A 1113 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7439 (tt) REVERT: A 1166 MET cc_start: 0.5703 (OUTLIER) cc_final: 0.4932 (pmm) outliers start: 14 outliers final: 11 residues processed: 103 average time/residue: 1.5473 time to fit residues: 180.1964 Evaluate side-chains 107 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1204 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 9722 Z= 0.371 Angle : 0.757 11.761 13184 Z= 0.405 Chirality : 0.056 1.174 1524 Planarity : 0.007 0.053 1639 Dihedral : 7.414 99.294 1308 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.94 % Allowed : 14.42 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.90 (0.22), residues: 1180 helix: -0.73 (0.16), residues: 759 sheet: 0.36 (0.60), residues: 55 loop : -0.00 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 483 HIS 0.008 0.001 HIS A 153 PHE 0.023 0.002 PHE A 352 TYR 0.018 0.002 TYR A 881 ARG 0.006 0.000 ARG A1251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5699 (tm-30) REVERT: A 241 MET cc_start: 0.5648 (OUTLIER) cc_final: 0.4927 (mpt) REVERT: A 312 ARG cc_start: 0.6867 (mtt-85) cc_final: 0.6525 (mmp80) REVERT: A 319 MET cc_start: 0.7456 (mmm) cc_final: 0.7140 (mmt) REVERT: A 1045 ASN cc_start: 0.7863 (t0) cc_final: 0.7291 (t0) REVERT: A 1166 MET cc_start: 0.5656 (OUTLIER) cc_final: 0.4790 (pmm) outliers start: 20 outliers final: 14 residues processed: 106 average time/residue: 1.5622 time to fit residues: 187.1241 Evaluate side-chains 106 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1192 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 9722 Z= 0.371 Angle : 0.757 11.761 13184 Z= 0.405 Chirality : 0.056 1.174 1524 Planarity : 0.007 0.053 1639 Dihedral : 7.417 99.294 1308 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.65 % Allowed : 15.00 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.90 (0.22), residues: 1180 helix: -0.73 (0.16), residues: 759 sheet: 0.36 (0.60), residues: 55 loop : -0.00 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 483 HIS 0.008 0.001 HIS A 153 PHE 0.023 0.002 PHE A 352 TYR 0.018 0.002 TYR A 881 ARG 0.006 0.000 ARG A1251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.518 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 121 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5699 (tm-30) REVERT: A 241 MET cc_start: 0.5647 (OUTLIER) cc_final: 0.4927 (mpt) REVERT: A 312 ARG cc_start: 0.6867 (mtt-85) cc_final: 0.6525 (mmp80) REVERT: A 319 MET cc_start: 0.7457 (mmm) cc_final: 0.7140 (mmt) REVERT: A 1045 ASN cc_start: 0.7863 (t0) cc_final: 0.7291 (t0) REVERT: A 1166 MET cc_start: 0.5655 (OUTLIER) cc_final: 0.4790 (pmm) outliers start: 17 outliers final: 14 residues processed: 101 average time/residue: 1.5829 time to fit residues: 183.2431 Evaluate side-chains 106 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1192 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 10 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 9722 Z= 0.371 Angle : 0.757 11.761 13184 Z= 0.405 Chirality : 0.056 1.174 1524 Planarity : 0.007 0.053 1639 Dihedral : 7.414 99.294 1308 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.65 % Allowed : 15.00 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.90 (0.22), residues: 1180 helix: -0.73 (0.16), residues: 759 sheet: 0.36 (0.60), residues: 55 loop : -0.00 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 483 HIS 0.008 0.001 HIS A 153 PHE 0.023 0.002 PHE A 352 TYR 0.018 0.002 TYR A 881 ARG 0.006 0.000 ARG A1251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.456 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 121 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5699 (tm-30) REVERT: A 241 MET cc_start: 0.5647 (OUTLIER) cc_final: 0.4927 (mpt) REVERT: A 312 ARG cc_start: 0.6867 (mtt-85) cc_final: 0.6525 (mmp80) REVERT: A 319 MET cc_start: 0.7457 (mmm) cc_final: 0.7140 (mmt) REVERT: A 1045 ASN cc_start: 0.7863 (t0) cc_final: 0.7291 (t0) REVERT: A 1166 MET cc_start: 0.5655 (OUTLIER) cc_final: 0.4790 (pmm) outliers start: 17 outliers final: 14 residues processed: 101 average time/residue: 1.5346 time to fit residues: 176.3940 Evaluate side-chains 106 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1192 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.0670 chunk 63 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 9722 Z= 0.371 Angle : 0.757 11.762 13184 Z= 0.405 Chirality : 0.056 1.174 1524 Planarity : 0.007 0.053 1639 Dihedral : 7.424 99.294 1308 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.65 % Allowed : 15.00 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.90 (0.22), residues: 1180 helix: -0.73 (0.16), residues: 759 sheet: 0.36 (0.60), residues: 55 loop : -0.00 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 483 HIS 0.008 0.001 HIS A 153 PHE 0.023 0.002 PHE A 352 TYR 0.018 0.002 TYR A 881 ARG 0.006 0.000 ARG A1251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.455 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 121 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5699 (tm-30) REVERT: A 241 MET cc_start: 0.5647 (OUTLIER) cc_final: 0.4927 (mpt) REVERT: A 312 ARG cc_start: 0.6867 (mtt-85) cc_final: 0.6525 (mmp80) REVERT: A 319 MET cc_start: 0.7457 (mmm) cc_final: 0.7140 (mmt) REVERT: A 1045 ASN cc_start: 0.7863 (t0) cc_final: 0.7291 (t0) REVERT: A 1166 MET cc_start: 0.5655 (OUTLIER) cc_final: 0.4790 (pmm) outliers start: 17 outliers final: 14 residues processed: 101 average time/residue: 1.5508 time to fit residues: 177.9811 Evaluate side-chains 106 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1192 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 9722 Z= 0.371 Angle : 0.758 11.768 13184 Z= 0.405 Chirality : 0.056 1.173 1524 Planarity : 0.007 0.053 1639 Dihedral : 7.385 99.293 1308 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.65 % Allowed : 15.00 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.90 (0.22), residues: 1180 helix: -0.73 (0.16), residues: 759 sheet: 0.36 (0.60), residues: 55 loop : -0.00 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 483 HIS 0.008 0.001 HIS A 153 PHE 0.023 0.002 PHE A 352 TYR 0.018 0.002 TYR A 881 ARG 0.006 0.000 ARG A1251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.546 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 121 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5699 (tm-30) REVERT: A 241 MET cc_start: 0.5647 (OUTLIER) cc_final: 0.4927 (mpt) REVERT: A 312 ARG cc_start: 0.6867 (mtt-85) cc_final: 0.6525 (mmp80) REVERT: A 319 MET cc_start: 0.7457 (mmm) cc_final: 0.7140 (mmt) REVERT: A 1045 ASN cc_start: 0.7863 (t0) cc_final: 0.7291 (t0) REVERT: A 1166 MET cc_start: 0.5655 (OUTLIER) cc_final: 0.4790 (pmm) outliers start: 17 outliers final: 14 residues processed: 101 average time/residue: 1.5433 time to fit residues: 177.0423 Evaluate side-chains 106 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1192 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.227799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.165134 restraints weight = 36097.410| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.45 r_work: 0.3895 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9722 Z= 0.245 Angle : 0.713 9.098 13184 Z= 0.379 Chirality : 0.043 0.318 1524 Planarity : 0.006 0.055 1639 Dihedral : 6.567 86.733 1308 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.94 % Allowed : 14.62 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.78 (0.22), residues: 1180 helix: -0.68 (0.17), residues: 765 sheet: 0.46 (0.63), residues: 55 loop : 0.16 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 483 HIS 0.008 0.002 HIS A 710 PHE 0.017 0.002 PHE A 352 TYR 0.016 0.002 TYR A 881 ARG 0.011 0.001 ARG A 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6113.64 seconds wall clock time: 111 minutes 5.98 seconds (6665.98 seconds total)