Starting phenix.real_space_refine on Thu Jul 2 19:40:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wfu_65937/07_2026/9wfu_65937.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wfu_65937/07_2026/9wfu_65937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wfu_65937/07_2026/9wfu_65937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wfu_65937/07_2026/9wfu_65937.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wfu_65937/07_2026/9wfu_65937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wfu_65937/07_2026/9wfu_65937.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 6121 2.51 5 N 1685 2.21 5 O 1776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9628 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1210, 9564 Classifications: {'peptide': 1210} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 1172} Chain breaks: 3 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.74, per 1000 atoms: 0.18 Number of scatterers: 9628 At special positions: 0 Unit cell: (79.18, 87.74, 144.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 6 15.00 Mg 2 11.99 O 1776 8.00 N 1685 7.00 C 6121 6.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 325.2 milliseconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2248 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 6 sheets defined 66.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 87 through 100 removed outlier: 3.635A pdb=" N GLN A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 96 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 139 removed outlier: 3.697A pdb=" N LEU A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 150 Processing helix chain 'A' and resid 152 through 191 removed outlier: 4.145A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.628A pdb=" N LYS A 197 " --> pdb=" O MET A 193 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER A 199 " --> pdb=" O TYR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 215 through 248 removed outlier: 3.617A pdb=" N ASP A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TRP A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 269 removed outlier: 4.038A pdb=" N PHE A 254 " --> pdb=" O PRO A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 298 removed outlier: 3.795A pdb=" N GLU A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 307 through 333 removed outlier: 3.522A pdb=" N ASN A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 345 removed outlier: 3.571A pdb=" N LEU A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 355 Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 378 through 426 removed outlier: 4.449A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARG A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 495 removed outlier: 3.786A pdb=" N PHE A 491 " --> pdb=" O LYS A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 538 Processing helix chain 'A' and resid 550 through 561 Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.574A pdb=" N LEU A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 582 removed outlier: 4.109A pdb=" N GLU A 581 " --> pdb=" O ASN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 599 Processing helix chain 'A' and resid 613 through 627 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 682 through 698 removed outlier: 3.685A pdb=" N ASP A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN A 691 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 757 through 766 Processing helix chain 'A' and resid 770 through 793 Processing helix chain 'A' and resid 799 through 812 Processing helix chain 'A' and resid 816 through 843 removed outlier: 3.751A pdb=" N ARG A 841 " --> pdb=" O GLN A 837 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN A 842 " --> pdb=" O HIS A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 854 removed outlier: 3.959A pdb=" N LYS A 851 " --> pdb=" O ASN A 847 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 853 " --> pdb=" O PHE A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 removed outlier: 3.565A pdb=" N ARG A 865 " --> pdb=" O ASP A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 903 removed outlier: 3.896A pdb=" N GLU A 871 " --> pdb=" O THR A 867 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 873 " --> pdb=" O ASP A 869 " (cutoff:3.500A) Proline residue: A 887 - end of helix removed outlier: 4.281A pdb=" N LEU A 900 " --> pdb=" O TRP A 896 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 925 removed outlier: 3.728A pdb=" N ALA A 908 " --> pdb=" O GLN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 952 removed outlier: 3.736A pdb=" N LEU A 931 " --> pdb=" O ASP A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 960 Processing helix chain 'A' and resid 961 through 992 removed outlier: 3.609A pdb=" N LEU A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 999 Processing helix chain 'A' and resid 1000 through 1016 removed outlier: 3.822A pdb=" N ASN A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1068 removed outlier: 3.770A pdb=" N HIS A1032 " --> pdb=" O GLY A1028 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N HIS A1055 " --> pdb=" O ILE A1051 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A1057 " --> pdb=" O GLU A1053 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY A1063 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY A1064 " --> pdb=" O GLU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1077 Processing helix chain 'A' and resid 1137 through 1144 Processing helix chain 'A' and resid 1185 through 1190 Processing helix chain 'A' and resid 1193 through 1205 Processing helix chain 'A' and resid 1213 through 1229 removed outlier: 4.019A pdb=" N ILE A1217 " --> pdb=" O GLU A1213 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A1225 " --> pdb=" O HIS A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1238 removed outlier: 4.066A pdb=" N LEU A1235 " --> pdb=" O LEU A1231 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP A1238 " --> pdb=" O LEU A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1244 removed outlier: 3.650A pdb=" N ASP A1243 " --> pdb=" O GLY A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1269 Processing helix chain 'A' and resid 1283 through 1298 removed outlier: 4.200A pdb=" N GLU A1288 " --> pdb=" O VAL A1284 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN A1289 " --> pdb=" O ASP A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1311 Processing sheet with id=AA1, first strand: chain 'A' and resid 467 through 472 removed outlier: 7.350A pdb=" N LEU A 469 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER A 451 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL A 471 " --> pdb=" O GLU A 449 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLU A 449 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 521 removed outlier: 6.174A pdb=" N PHE A 519 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ASP A 606 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL A 521 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A 477 " --> pdb=" O THR A 633 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 478 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LEU A 650 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR A 480 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1119 through 1121 Processing sheet with id=AA4, first strand: chain 'A' and resid 1102 through 1106 removed outlier: 6.909A pdb=" N ILE A1104 " --> pdb=" O SER A1114 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER A1114 " --> pdb=" O ILE A1104 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR A1106 " --> pdb=" O MET A1112 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N MET A1112 " --> pdb=" O THR A1106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1170 through 1173 Processing sheet with id=AA6, first strand: chain 'A' and resid 1316 through 1320 removed outlier: 3.966A pdb=" N GLU A1317 " --> pdb=" O ARG A1330 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1692 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: 1.19 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3156 1.34 - 1.46: 2200 1.46 - 1.58: 4388 1.58 - 1.70: 6 1.70 - 1.82: 67 Bond restraints: 9817 Sorted by residual: bond pdb=" N PHE A 145 " pdb=" CA PHE A 145 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.17e+00 bond pdb=" N GLN A 523 " pdb=" CA GLN A 523 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.56e+00 bond pdb=" N GLU A 871 " pdb=" CA GLU A 871 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.19e-02 7.06e+03 4.10e+00 bond pdb=" N GLN A1094 " pdb=" CA GLN A1094 " ideal model delta sigma weight residual 1.462 1.488 -0.025 1.31e-02 5.83e+03 3.69e+00 bond pdb=" CB MET A 914 " pdb=" CG MET A 914 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.04e+00 ... (remaining 9812 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 13224 3.41 - 6.81: 52 6.81 - 10.22: 7 10.22 - 13.63: 0 13.63 - 17.03: 1 Bond angle restraints: 13284 Sorted by residual: angle pdb=" C ARG A 698 " pdb=" CA ARG A 698 " pdb=" CB ARG A 698 " ideal model delta sigma weight residual 116.54 110.21 6.33 1.15e+00 7.56e-01 3.03e+01 angle pdb=" CA LEU A 133 " pdb=" CB LEU A 133 " pdb=" CG LEU A 133 " ideal model delta sigma weight residual 116.30 133.33 -17.03 3.50e+00 8.16e-02 2.37e+01 angle pdb=" C THR A 703 " pdb=" CA THR A 703 " pdb=" CB THR A 703 " ideal model delta sigma weight residual 117.23 111.28 5.95 1.36e+00 5.41e-01 1.91e+01 angle pdb=" CA ARG A 698 " pdb=" C ARG A 698 " pdb=" N LYS A 699 " ideal model delta sigma weight residual 119.52 116.40 3.12 7.90e-01 1.60e+00 1.56e+01 angle pdb=" CA THR A 703 " pdb=" C THR A 703 " pdb=" N ASN A 704 " ideal model delta sigma weight residual 119.98 117.12 2.86 8.50e-01 1.38e+00 1.13e+01 ... (remaining 13279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 4972 17.18 - 34.36: 670 34.36 - 51.54: 213 51.54 - 68.72: 51 68.72 - 85.90: 15 Dihedral angle restraints: 5921 sinusoidal: 2432 harmonic: 3489 Sorted by residual: dihedral pdb=" CA PHE A1069 " pdb=" C PHE A1069 " pdb=" N GLU A1070 " pdb=" CA GLU A1070 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA LEU A1111 " pdb=" C LEU A1111 " pdb=" N MET A1112 " pdb=" CA MET A1112 " ideal model delta harmonic sigma weight residual 180.00 -160.65 -19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ALA A 812 " pdb=" C ALA A 812 " pdb=" N SER A 813 " pdb=" CA SER A 813 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 5918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1392 0.069 - 0.138: 109 0.138 - 0.208: 5 0.208 - 0.277: 3 0.277 - 0.346: 1 Chirality restraints: 1510 Sorted by residual: chirality pdb=" CG LEU A 133 " pdb=" CB LEU A 133 " pdb=" CD1 LEU A 133 " pdb=" CD2 LEU A 133 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA LEU A1023 " pdb=" N LEU A1023 " pdb=" C LEU A1023 " pdb=" CB LEU A1023 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB ILE A 891 " pdb=" CA ILE A 891 " pdb=" CG1 ILE A 891 " pdb=" CG2 ILE A 891 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1507 not shown) Planarity restraints: 1675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1048 " 0.018 2.00e-02 2.50e+03 1.54e-02 4.17e+00 pdb=" CG PHE A1048 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A1048 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A1048 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A1048 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1048 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A1048 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 732 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO A 733 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 733 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 733 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1106 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A1107 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A1107 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1107 " 0.017 5.00e-02 4.00e+02 ... (remaining 1672 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 23 2.34 - 2.98: 4923 2.98 - 3.62: 14863 3.62 - 4.26: 21814 4.26 - 4.90: 37159 Nonbonded interactions: 78782 Sorted by model distance: nonbonded pdb=" OE1 GLU A1287 " pdb=" NH1 ARG A1307 " model vdw 1.700 3.120 nonbonded pdb=" NE2 GLN A1175 " pdb=" OE1 GLU A1277 " model vdw 1.901 3.120 nonbonded pdb=" O1G ATP A1401 " pdb="MG MG A1403 " model vdw 1.938 2.170 nonbonded pdb=" O3G ATP A1402 " pdb="MG MG A1404 " model vdw 1.949 2.170 nonbonded pdb=" OG SER A 488 " pdb=" NE2 GLN A 523 " model vdw 1.985 3.120 ... (remaining 78777 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=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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.080 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 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 : 0.003 0.043 9817 Z= 0.135 Angle : 0.602 17.032 13284 Z= 0.315 Chirality : 0.041 0.346 1510 Planarity : 0.003 0.038 1675 Dihedral : 18.070 85.899 3673 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.10 % Allowed : 29.59 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.26), residues: 1202 helix: 1.84 (0.20), residues: 715 sheet: -0.31 (0.65), residues: 77 loop : -1.49 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 268 TYR 0.021 0.001 TYR A 447 PHE 0.034 0.001 PHE A1048 TRP 0.007 0.001 TRP A 896 HIS 0.004 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 9817) covalent geometry : angle 0.60208 / 0.31 (13284) hydrogen bonds : bond 0.14707 / 10.06 ( 575) hydrogen bonds : angle 5.69480 / 4.06 ( 1692) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 110 LEU cc_start: 0.7245 (tp) cc_final: 0.7027 (mt) REVERT: A 132 PHE cc_start: 0.6959 (m-10) cc_final: 0.6655 (m-10) REVERT: A 138 PHE cc_start: 0.6913 (t80) cc_final: 0.6425 (t80) REVERT: A 149 ILE cc_start: 0.7283 (mt) cc_final: 0.6980 (tp) REVERT: A 163 HIS cc_start: 0.6700 (m-70) cc_final: 0.6452 (m170) REVERT: A 251 LYS cc_start: 0.7782 (mmmm) cc_final: 0.7538 (pttm) REVERT: A 278 MET cc_start: 0.8393 (tpp) cc_final: 0.8169 (tpp) REVERT: A 281 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7967 (tt0) REVERT: A 313 SER cc_start: 0.8207 (t) cc_final: 0.7902 (m) REVERT: A 317 GLN cc_start: 0.7883 (tp40) cc_final: 0.7496 (tt0) REVERT: A 341 ASP cc_start: 0.7275 (t0) cc_final: 0.6784 (t0) REVERT: A 377 MET cc_start: 0.1718 (tpt) cc_final: 0.0736 (tpp) REVERT: A 559 LYS cc_start: 0.7370 (ptmm) cc_final: 0.6931 (ptpt) REVERT: A 574 LYS cc_start: 0.5902 (pttt) cc_final: 0.5325 (tttp) REVERT: A 637 ARG cc_start: 0.6509 (mmp80) cc_final: 0.6044 (mmt-90) REVERT: A 659 HIS cc_start: 0.7326 (m90) cc_final: 0.6668 (m90) REVERT: A 713 GLN cc_start: 0.7028 (mp10) cc_final: 0.6816 (mp10) REVERT: A 747 MET cc_start: 0.7853 (ttm) cc_final: 0.7551 (ttm) REVERT: A 893 TRP cc_start: 0.7788 (t-100) cc_final: 0.7483 (t-100) REVERT: A 970 ASP cc_start: 0.8003 (m-30) cc_final: 0.7503 (m-30) REVERT: A 1046 MET cc_start: 0.6644 (mmt) cc_final: 0.6276 (mmt) REVERT: A 1053 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7827 (tm-30) REVERT: A 1119 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6969 (pm20) REVERT: A 1155 THR cc_start: 0.8141 (m) cc_final: 0.7764 (p) REVERT: A 1230 ARG cc_start: 0.7290 (mtt-85) cc_final: 0.6929 (mtt90) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.1027 time to fit residues: 29.7244 Evaluate side-chains 138 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 192 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 HIS A 333 HIS A 560 ASN A 713 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.163227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127175 restraints weight = 11569.615| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.03 r_work: 0.3289 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9817 Z= 0.154 Angle : 0.582 8.911 13284 Z= 0.298 Chirality : 0.040 0.234 1510 Planarity : 0.004 0.036 1675 Dihedral : 9.011 88.516 1392 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.13 % Allowed : 26.51 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.26), residues: 1202 helix: 1.94 (0.20), residues: 732 sheet: -0.36 (0.64), residues: 78 loop : -1.38 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 625 TYR 0.022 0.002 TYR A 447 PHE 0.019 0.001 PHE A1048 TRP 0.012 0.001 TRP A 242 HIS 0.004 0.001 HIS A 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 9817) covalent geometry : angle 0.58172 / 0.30 (13284) hydrogen bonds : bond 0.04271 / 2.86 ( 575) hydrogen bonds : angle 4.26891 / 3.08 ( 1692) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.267 Fit side-chains REVERT: A 110 LEU cc_start: 0.7555 (tp) cc_final: 0.7350 (mt) REVERT: A 128 LYS cc_start: 0.7255 (mtmt) cc_final: 0.6982 (mmmt) REVERT: A 192 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8263 (t0) REVERT: A 251 LYS cc_start: 0.7972 (mmmm) cc_final: 0.7536 (pttm) REVERT: A 281 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8455 (tt0) REVERT: A 317 GLN cc_start: 0.8467 (tp40) cc_final: 0.7852 (tt0) REVERT: A 339 ILE cc_start: 0.8724 (mt) cc_final: 0.8282 (mt) REVERT: A 377 MET cc_start: 0.1891 (tpt) cc_final: 0.1109 (tpp) REVERT: A 502 SER cc_start: 0.8343 (t) cc_final: 0.8107 (m) REVERT: A 559 LYS cc_start: 0.7838 (ptmm) cc_final: 0.7390 (ptpt) REVERT: A 574 LYS cc_start: 0.6346 (pttt) cc_final: 0.5513 (tttp) REVERT: A 625 ARG cc_start: 0.7946 (ptt180) cc_final: 0.7503 (mtt180) REVERT: A 627 MET cc_start: 0.7894 (ttm) cc_final: 0.7661 (ttp) REVERT: A 659 HIS cc_start: 0.7614 (m90) cc_final: 0.7097 (m90) REVERT: A 710 TYR cc_start: 0.4675 (OUTLIER) cc_final: 0.4327 (p90) REVERT: A 713 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6486 (pt0) REVERT: A 747 MET cc_start: 0.8312 (ttm) cc_final: 0.7878 (ttt) REVERT: A 910 LEU cc_start: 0.8050 (mt) cc_final: 0.7835 (tp) REVERT: A 914 MET cc_start: 0.6521 (mmt) cc_final: 0.6063 (mmm) REVERT: A 970 ASP cc_start: 0.8482 (m-30) cc_final: 0.8083 (m-30) REVERT: A 981 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7689 (tp) REVERT: A 999 LYS cc_start: 0.8158 (mmmm) cc_final: 0.7682 (mttt) REVERT: A 1053 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8073 (tm-30) REVERT: A 1061 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7660 (tt) REVERT: A 1112 MET cc_start: 0.7673 (ttp) cc_final: 0.7440 (ttm) REVERT: A 1230 ARG cc_start: 0.8160 (mtt-85) cc_final: 0.7850 (mtt90) outliers start: 43 outliers final: 17 residues processed: 180 average time/residue: 0.0919 time to fit residues: 23.1780 Evaluate side-chains 150 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 713 GLN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1234 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 44 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 HIS ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 ASN ** A1079 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 = 0.3801 r_free = 0.3801 target = 0.157346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120988 restraints weight = 11633.950| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.99 r_work: 0.3204 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9817 Z= 0.235 Angle : 0.625 8.863 13284 Z= 0.321 Chirality : 0.042 0.216 1510 Planarity : 0.004 0.040 1675 Dihedral : 9.046 89.639 1392 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.00 % Allowed : 25.17 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.25), residues: 1202 helix: 1.63 (0.19), residues: 741 sheet: -0.51 (0.63), residues: 79 loop : -1.51 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1330 TYR 0.024 0.002 TYR A 447 PHE 0.032 0.002 PHE A1048 TRP 0.011 0.001 TRP A 988 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.23 ( 9817) covalent geometry : angle 0.62518 / 0.32 (13284) hydrogen bonds : bond 0.04760 / 3.18 ( 575) hydrogen bonds : angle 4.27916 / 3.08 ( 1692) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 0.217 Fit side-chains REVERT: A 110 LEU cc_start: 0.7851 (tp) cc_final: 0.7546 (mt) REVERT: A 128 LYS cc_start: 0.7276 (mtmt) cc_final: 0.7025 (mtpp) REVERT: A 133 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7823 (mm) REVERT: A 192 ASN cc_start: 0.8796 (t0) cc_final: 0.8554 (t0) REVERT: A 251 LYS cc_start: 0.8034 (mmmm) cc_final: 0.7450 (pttm) REVERT: A 281 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8577 (tt0) REVERT: A 317 GLN cc_start: 0.8572 (tp40) cc_final: 0.7896 (tt0) REVERT: A 339 ILE cc_start: 0.8821 (mt) cc_final: 0.8415 (mt) REVERT: A 347 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8032 (mp) REVERT: A 377 MET cc_start: 0.2033 (tpt) cc_final: 0.0736 (tpp) REVERT: A 381 ILE cc_start: 0.5466 (OUTLIER) cc_final: 0.5097 (tp) REVERT: A 502 SER cc_start: 0.8492 (t) cc_final: 0.8270 (m) REVERT: A 559 LYS cc_start: 0.8073 (ptmm) cc_final: 0.7582 (ptpt) REVERT: A 574 LYS cc_start: 0.6347 (pttt) cc_final: 0.5377 (tttp) REVERT: A 616 MET cc_start: 0.7927 (tpp) cc_final: 0.7685 (tpp) REVERT: A 625 ARG cc_start: 0.7919 (ptt180) cc_final: 0.7654 (tpp80) REVERT: A 627 MET cc_start: 0.7983 (ttm) cc_final: 0.7772 (ttp) REVERT: A 659 HIS cc_start: 0.7727 (m90) cc_final: 0.7193 (m90) REVERT: A 660 TYR cc_start: 0.8231 (m-80) cc_final: 0.7978 (m-80) REVERT: A 747 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8044 (ttm) REVERT: A 970 ASP cc_start: 0.8649 (m-30) cc_final: 0.8239 (m-30) REVERT: A 981 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7817 (tp) REVERT: A 999 LYS cc_start: 0.8143 (mmmm) cc_final: 0.7711 (mttt) REVERT: A 1053 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8091 (tm-30) REVERT: A 1061 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7702 (tt) REVERT: A 1230 ARG cc_start: 0.8149 (mtt-85) cc_final: 0.7925 (mtt180) REVERT: A 1276 ASP cc_start: 0.8205 (t0) cc_final: 0.7929 (t0) REVERT: A 1330 ARG cc_start: 0.8293 (mmm160) cc_final: 0.7768 (mmt180) outliers start: 52 outliers final: 27 residues processed: 186 average time/residue: 0.0796 time to fit residues: 20.7164 Evaluate side-chains 159 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1234 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 82 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 ASN ** A1079 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 = 0.3818 r_free = 0.3818 target = 0.158908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123315 restraints weight = 11605.680| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.89 r_work: 0.3231 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9817 Z= 0.147 Angle : 0.558 7.606 13284 Z= 0.286 Chirality : 0.039 0.212 1510 Planarity : 0.004 0.041 1675 Dihedral : 8.623 89.656 1392 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.13 % Allowed : 26.90 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.25), residues: 1202 helix: 1.69 (0.19), residues: 749 sheet: -0.56 (0.63), residues: 79 loop : -1.47 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.020 0.002 TYR A 447 PHE 0.029 0.001 PHE A1048 TRP 0.008 0.001 TRP A 335 HIS 0.005 0.001 HIS A 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9817) covalent geometry : angle 0.55800 / 0.29 (13284) hydrogen bonds : bond 0.04207 / 2.81 ( 575) hydrogen bonds : angle 4.10228 / 2.96 ( 1692) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 0.274 Fit side-chains REVERT: A 104 MET cc_start: 0.8591 (tpt) cc_final: 0.8163 (mmm) REVERT: A 110 LEU cc_start: 0.7810 (tp) cc_final: 0.7526 (mt) REVERT: A 128 LYS cc_start: 0.7297 (mtmt) cc_final: 0.7041 (mtpp) REVERT: A 133 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7757 (mm) REVERT: A 192 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8572 (t0) REVERT: A 251 LYS cc_start: 0.8040 (mmmm) cc_final: 0.7463 (pttm) REVERT: A 281 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8663 (tt0) REVERT: A 339 ILE cc_start: 0.8760 (mt) cc_final: 0.8349 (mt) REVERT: A 377 MET cc_start: 0.1772 (tpt) cc_final: 0.0670 (tpp) REVERT: A 381 ILE cc_start: 0.5544 (OUTLIER) cc_final: 0.5229 (tp) REVERT: A 413 ASP cc_start: 0.8396 (t0) cc_final: 0.8019 (m-30) REVERT: A 502 SER cc_start: 0.8435 (t) cc_final: 0.8222 (m) REVERT: A 544 GLN cc_start: 0.7801 (mp10) cc_final: 0.7423 (pm20) REVERT: A 559 LYS cc_start: 0.8013 (ptmm) cc_final: 0.7548 (ptpt) REVERT: A 574 LYS cc_start: 0.6332 (pttt) cc_final: 0.5355 (tttp) REVERT: A 607 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7805 (mt0) REVERT: A 616 MET cc_start: 0.7837 (tpp) cc_final: 0.7629 (tpp) REVERT: A 625 ARG cc_start: 0.7833 (ptt180) cc_final: 0.7630 (tpp80) REVERT: A 627 MET cc_start: 0.7935 (ttm) cc_final: 0.7572 (ttp) REVERT: A 659 HIS cc_start: 0.7773 (m90) cc_final: 0.7262 (m90) REVERT: A 747 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7941 (ttt) REVERT: A 890 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7804 (t0) REVERT: A 970 ASP cc_start: 0.8569 (m-30) cc_final: 0.7980 (m-30) REVERT: A 981 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7724 (tp) REVERT: A 999 LYS cc_start: 0.8103 (mmmm) cc_final: 0.7679 (mttt) REVERT: A 1053 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8032 (tm-30) REVERT: A 1061 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7643 (tt) REVERT: A 1297 MET cc_start: 0.8720 (ttp) cc_final: 0.8444 (mtp) REVERT: A 1330 ARG cc_start: 0.8227 (mmm160) cc_final: 0.7555 (mmt180) outliers start: 43 outliers final: 24 residues processed: 164 average time/residue: 0.0856 time to fit residues: 19.3347 Evaluate side-chains 160 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1234 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 6 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 108 optimal weight: 0.3980 chunk 95 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 384 HIS ** A1079 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 = 0.3828 r_free = 0.3828 target = 0.160006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123562 restraints weight = 11535.024| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.07 r_work: 0.3238 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9817 Z= 0.125 Angle : 0.526 7.284 13284 Z= 0.272 Chirality : 0.039 0.226 1510 Planarity : 0.003 0.044 1675 Dihedral : 8.427 87.426 1392 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.51 % Allowed : 26.99 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.25), residues: 1202 helix: 1.84 (0.19), residues: 749 sheet: -0.52 (0.64), residues: 78 loop : -1.49 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.019 0.001 TYR A 447 PHE 0.023 0.001 PHE A1048 TRP 0.007 0.001 TRP A 335 HIS 0.004 0.001 HIS A 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9817) covalent geometry : angle 0.52576 / 0.27 (13284) hydrogen bonds : bond 0.03931 / 2.62 ( 575) hydrogen bonds : angle 4.00787 / 2.90 ( 1692) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.8557 (tpt) cc_final: 0.8176 (mmm) REVERT: A 110 LEU cc_start: 0.7782 (tp) cc_final: 0.7508 (mt) REVERT: A 128 LYS cc_start: 0.7235 (mtmt) cc_final: 0.6992 (mtpp) REVERT: A 133 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7708 (mm) REVERT: A 251 LYS cc_start: 0.8010 (mmmm) cc_final: 0.7411 (pttm) REVERT: A 281 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8684 (tt0) REVERT: A 326 MET cc_start: 0.8601 (tpp) cc_final: 0.7963 (mmm) REVERT: A 339 ILE cc_start: 0.8763 (mt) cc_final: 0.8358 (mt) REVERT: A 377 MET cc_start: 0.1967 (tpt) cc_final: 0.1033 (tpp) REVERT: A 381 ILE cc_start: 0.5545 (OUTLIER) cc_final: 0.5273 (tp) REVERT: A 413 ASP cc_start: 0.8421 (t0) cc_final: 0.8048 (m-30) REVERT: A 544 GLN cc_start: 0.7799 (mp10) cc_final: 0.7376 (pm20) REVERT: A 555 VAL cc_start: 0.7566 (t) cc_final: 0.6932 (m) REVERT: A 559 LYS cc_start: 0.7840 (ptmm) cc_final: 0.7441 (ptpt) REVERT: A 607 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7775 (mt0) REVERT: A 625 ARG cc_start: 0.7784 (ptt180) cc_final: 0.7530 (tpp80) REVERT: A 627 MET cc_start: 0.7862 (ttm) cc_final: 0.7376 (ttp) REVERT: A 659 HIS cc_start: 0.7753 (m90) cc_final: 0.7231 (m90) REVERT: A 747 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7981 (ttt) REVERT: A 778 ASP cc_start: 0.8030 (t70) cc_final: 0.7673 (t0) REVERT: A 816 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8127 (mp) REVERT: A 890 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7812 (t0) REVERT: A 981 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7704 (tp) REVERT: A 999 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7716 (mttt) REVERT: A 1053 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8014 (tm-30) REVERT: A 1330 ARG cc_start: 0.8269 (mmm160) cc_final: 0.7553 (mmt180) outliers start: 47 outliers final: 27 residues processed: 175 average time/residue: 0.0985 time to fit residues: 23.9628 Evaluate side-chains 159 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1286 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 55 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 384 HIS A 607 GLN A 684 GLN ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118993 restraints weight = 11680.366| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.04 r_work: 0.3173 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9817 Z= 0.232 Angle : 0.608 8.721 13284 Z= 0.313 Chirality : 0.042 0.252 1510 Planarity : 0.004 0.048 1675 Dihedral : 8.776 87.089 1392 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.67 % Allowed : 25.26 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.25), residues: 1202 helix: 1.49 (0.19), residues: 748 sheet: -0.71 (0.62), residues: 79 loop : -1.65 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1185 TYR 0.021 0.002 TYR A 447 PHE 0.021 0.002 PHE A1048 TRP 0.008 0.001 TRP A 988 HIS 0.021 0.002 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.23 ( 9817) covalent geometry : angle 0.60829 / 0.31 (13284) hydrogen bonds : bond 0.04647 / 3.11 ( 575) hydrogen bonds : angle 4.17532 / 3.02 ( 1692) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 133 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.8641 (tpt) cc_final: 0.8222 (mmm) REVERT: A 110 LEU cc_start: 0.7925 (tp) cc_final: 0.7585 (mt) REVERT: A 128 LYS cc_start: 0.7293 (mtmt) cc_final: 0.7043 (mtpp) REVERT: A 133 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7710 (mm) REVERT: A 192 ASN cc_start: 0.8890 (t0) cc_final: 0.8640 (t0) REVERT: A 251 LYS cc_start: 0.8020 (mmmm) cc_final: 0.7453 (pttm) REVERT: A 281 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8720 (tt0) REVERT: A 339 ILE cc_start: 0.8839 (mt) cc_final: 0.8410 (mt) REVERT: A 377 MET cc_start: 0.1991 (tpt) cc_final: 0.1102 (tpp) REVERT: A 381 ILE cc_start: 0.5695 (OUTLIER) cc_final: 0.5431 (tp) REVERT: A 382 ARG cc_start: 0.7042 (tpt-90) cc_final: 0.6801 (mtp180) REVERT: A 413 ASP cc_start: 0.8499 (t0) cc_final: 0.8078 (m-30) REVERT: A 559 LYS cc_start: 0.7982 (ptmm) cc_final: 0.7491 (ptpt) REVERT: A 625 ARG cc_start: 0.7787 (ptt180) cc_final: 0.7567 (tpp80) REVERT: A 659 HIS cc_start: 0.7799 (m90) cc_final: 0.7267 (m90) REVERT: A 747 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8051 (ttm) REVERT: A 778 ASP cc_start: 0.8059 (t70) cc_final: 0.7819 (t0) REVERT: A 816 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8210 (mp) REVERT: A 819 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8466 (m) REVERT: A 890 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7814 (t0) REVERT: A 970 ASP cc_start: 0.8711 (m-30) cc_final: 0.8254 (m-30) REVERT: A 981 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7815 (tp) REVERT: A 999 LYS cc_start: 0.8221 (mmmm) cc_final: 0.7768 (mttt) REVERT: A 1012 LEU cc_start: 0.7371 (mm) cc_final: 0.7162 (mm) REVERT: A 1053 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7953 (tm-30) REVERT: A 1276 ASP cc_start: 0.8312 (t0) cc_final: 0.8008 (t0) REVERT: A 1330 ARG cc_start: 0.8322 (mmm160) cc_final: 0.7417 (mmt180) REVERT: A 1331 SER cc_start: 0.8017 (t) cc_final: 0.7717 (m) outliers start: 59 outliers final: 36 residues processed: 174 average time/residue: 0.1034 time to fit residues: 25.0498 Evaluate side-chains 171 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1286 VAL Chi-restraints excluded: chain A residue 1303 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 107 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 105 optimal weight: 0.0770 chunk 114 optimal weight: 0.0070 chunk 28 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 163 HIS A 188 HIS ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 936 GLN A1079 GLN A1175 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.159386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.122919 restraints weight = 11477.160| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.05 r_work: 0.3228 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9817 Z= 0.117 Angle : 0.525 7.406 13284 Z= 0.275 Chirality : 0.038 0.272 1510 Planarity : 0.003 0.047 1675 Dihedral : 8.285 84.711 1392 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.13 % Allowed : 27.19 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.25), residues: 1202 helix: 1.80 (0.19), residues: 751 sheet: -0.64 (0.62), residues: 78 loop : -1.67 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 533 TYR 0.018 0.001 TYR A 447 PHE 0.019 0.001 PHE A 145 TRP 0.007 0.001 TRP A 335 HIS 0.009 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 9817) covalent geometry : angle 0.52463 / 0.27 (13284) hydrogen bonds : bond 0.03904 / 2.62 ( 575) hydrogen bonds : angle 3.99279 / 2.89 ( 1692) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8480 (tp) cc_final: 0.8210 (tp) REVERT: A 104 MET cc_start: 0.8585 (tpt) cc_final: 0.8189 (mmm) REVERT: A 110 LEU cc_start: 0.7807 (tp) cc_final: 0.7528 (mt) REVERT: A 128 LYS cc_start: 0.7277 (mtmt) cc_final: 0.6909 (mmmt) REVERT: A 133 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7533 (mm) REVERT: A 192 ASN cc_start: 0.8878 (t0) cc_final: 0.8594 (t0) REVERT: A 251 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7461 (pttm) REVERT: A 281 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8613 (tt0) REVERT: A 326 MET cc_start: 0.8589 (tpp) cc_final: 0.7941 (mmm) REVERT: A 338 MET cc_start: 0.8878 (ptp) cc_final: 0.8627 (ptm) REVERT: A 339 ILE cc_start: 0.8757 (mt) cc_final: 0.8324 (mt) REVERT: A 377 MET cc_start: 0.1861 (tpt) cc_final: 0.1140 (tpp) REVERT: A 381 ILE cc_start: 0.5600 (OUTLIER) cc_final: 0.5364 (tp) REVERT: A 387 VAL cc_start: 0.7566 (OUTLIER) cc_final: 0.7349 (p) REVERT: A 413 ASP cc_start: 0.8379 (t0) cc_final: 0.7996 (m-30) REVERT: A 517 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7476 (mm-30) REVERT: A 544 GLN cc_start: 0.7948 (mp10) cc_final: 0.7565 (pm20) REVERT: A 554 MET cc_start: 0.8011 (ttt) cc_final: 0.7607 (mmm) REVERT: A 555 VAL cc_start: 0.7756 (t) cc_final: 0.7093 (m) REVERT: A 559 LYS cc_start: 0.7785 (ptmm) cc_final: 0.7346 (ptpt) REVERT: A 625 ARG cc_start: 0.7622 (ptt180) cc_final: 0.7395 (tpp80) REVERT: A 659 HIS cc_start: 0.7777 (m90) cc_final: 0.7267 (m90) REVERT: A 747 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7927 (ttt) REVERT: A 778 ASP cc_start: 0.7978 (t70) cc_final: 0.7637 (t0) REVERT: A 816 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8134 (mp) REVERT: A 884 MET cc_start: 0.8014 (tpt) cc_final: 0.7747 (ttm) REVERT: A 890 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7782 (t0) REVERT: A 981 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7700 (tp) REVERT: A 999 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7743 (mttt) REVERT: A 1012 LEU cc_start: 0.7401 (mm) cc_final: 0.7177 (mm) REVERT: A 1053 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7927 (tm-30) REVERT: A 1330 ARG cc_start: 0.8254 (mmm160) cc_final: 0.7423 (mmt180) REVERT: A 1331 SER cc_start: 0.7941 (t) cc_final: 0.7704 (m) outliers start: 43 outliers final: 27 residues processed: 167 average time/residue: 0.0938 time to fit residues: 22.4013 Evaluate side-chains 162 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1286 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 0.0670 chunk 20 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN A1079 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.159338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.122960 restraints weight = 11559.044| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.06 r_work: 0.3228 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9817 Z= 0.130 Angle : 0.524 7.438 13284 Z= 0.275 Chirality : 0.039 0.280 1510 Planarity : 0.003 0.047 1675 Dihedral : 8.235 83.963 1392 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.13 % Allowed : 26.80 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.25), residues: 1202 helix: 1.89 (0.19), residues: 749 sheet: -0.79 (0.61), residues: 79 loop : -1.69 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.019 0.001 TYR A 447 PHE 0.017 0.001 PHE A1048 TRP 0.010 0.001 TRP A 988 HIS 0.012 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9817) covalent geometry : angle 0.52445 / 0.27 (13284) hydrogen bonds : bond 0.03907 / 2.62 ( 575) hydrogen bonds : angle 3.95672 / 2.87 ( 1692) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8490 (tp) cc_final: 0.8207 (tp) REVERT: A 104 MET cc_start: 0.8574 (tpt) cc_final: 0.8188 (mmm) REVERT: A 110 LEU cc_start: 0.7815 (tp) cc_final: 0.7532 (mt) REVERT: A 128 LYS cc_start: 0.7239 (mtmt) cc_final: 0.7013 (mtpp) REVERT: A 133 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7829 (mt) REVERT: A 192 ASN cc_start: 0.8876 (t0) cc_final: 0.8598 (t0) REVERT: A 251 LYS cc_start: 0.7984 (mmmm) cc_final: 0.7455 (pttm) REVERT: A 281 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8632 (tt0) REVERT: A 326 MET cc_start: 0.8594 (tpp) cc_final: 0.7947 (mmm) REVERT: A 339 ILE cc_start: 0.8759 (mt) cc_final: 0.8321 (mt) REVERT: A 377 MET cc_start: 0.2057 (tpt) cc_final: 0.1336 (tpp) REVERT: A 381 ILE cc_start: 0.5623 (OUTLIER) cc_final: 0.5398 (tp) REVERT: A 413 ASP cc_start: 0.8397 (t0) cc_final: 0.8013 (m-30) REVERT: A 517 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7535 (mm-30) REVERT: A 544 GLN cc_start: 0.7970 (mp10) cc_final: 0.7565 (pm20) REVERT: A 554 MET cc_start: 0.7874 (ttt) cc_final: 0.7496 (mmm) REVERT: A 555 VAL cc_start: 0.7697 (t) cc_final: 0.7059 (m) REVERT: A 559 LYS cc_start: 0.7826 (ptmm) cc_final: 0.7353 (ptpt) REVERT: A 625 ARG cc_start: 0.7672 (ptt180) cc_final: 0.7352 (tpp80) REVERT: A 659 HIS cc_start: 0.7742 (m90) cc_final: 0.7267 (m90) REVERT: A 747 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7924 (ttt) REVERT: A 778 ASP cc_start: 0.8022 (t70) cc_final: 0.7698 (t0) REVERT: A 799 PHE cc_start: 0.5191 (OUTLIER) cc_final: 0.4931 (m-80) REVERT: A 816 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8176 (mp) REVERT: A 884 MET cc_start: 0.8043 (tpt) cc_final: 0.7762 (ttm) REVERT: A 890 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7775 (t0) REVERT: A 914 MET cc_start: 0.6260 (tpt) cc_final: 0.5850 (tpt) REVERT: A 981 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7725 (tp) REVERT: A 999 LYS cc_start: 0.8134 (mmmm) cc_final: 0.7733 (mttt) REVERT: A 1012 LEU cc_start: 0.7501 (mm) cc_final: 0.7260 (mm) REVERT: A 1053 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7908 (tm-30) REVERT: A 1330 ARG cc_start: 0.8289 (mmm160) cc_final: 0.7437 (mmt180) REVERT: A 1331 SER cc_start: 0.7946 (t) cc_final: 0.7649 (m) outliers start: 43 outliers final: 30 residues processed: 168 average time/residue: 0.0948 time to fit residues: 22.7208 Evaluate side-chains 168 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1163 GLU Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1286 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 56 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 HIS ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.159875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123604 restraints weight = 11462.632| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.05 r_work: 0.3237 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9817 Z= 0.120 Angle : 0.514 7.457 13284 Z= 0.269 Chirality : 0.038 0.289 1510 Planarity : 0.003 0.047 1675 Dihedral : 8.077 81.768 1392 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.03 % Allowed : 26.61 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.25), residues: 1202 helix: 1.95 (0.19), residues: 748 sheet: -0.74 (0.61), residues: 79 loop : -1.68 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.018 0.001 TYR A 447 PHE 0.015 0.001 PHE A1048 TRP 0.009 0.001 TRP A 988 HIS 0.007 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9817) covalent geometry : angle 0.51385 / 0.27 (13284) hydrogen bonds : bond 0.03821 / 2.57 ( 575) hydrogen bonds : angle 3.93212 / 2.85 ( 1692) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.8610 (tpt) cc_final: 0.8228 (mmm) REVERT: A 110 LEU cc_start: 0.7802 (tp) cc_final: 0.7521 (mt) REVERT: A 128 LYS cc_start: 0.7238 (mtmt) cc_final: 0.7012 (mtpp) REVERT: A 133 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7819 (mt) REVERT: A 192 ASN cc_start: 0.8869 (t0) cc_final: 0.8572 (t0) REVERT: A 251 LYS cc_start: 0.7963 (mmmm) cc_final: 0.7440 (pttm) REVERT: A 326 MET cc_start: 0.8583 (tpp) cc_final: 0.7938 (mmm) REVERT: A 339 ILE cc_start: 0.8759 (mt) cc_final: 0.8321 (mt) REVERT: A 377 MET cc_start: 0.2034 (tpt) cc_final: 0.1359 (tpp) REVERT: A 381 ILE cc_start: 0.5626 (OUTLIER) cc_final: 0.5376 (tp) REVERT: A 413 ASP cc_start: 0.8380 (t0) cc_final: 0.7948 (m-30) REVERT: A 517 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7505 (mm-30) REVERT: A 544 GLN cc_start: 0.7961 (mp10) cc_final: 0.7563 (pm20) REVERT: A 554 MET cc_start: 0.7948 (ttt) cc_final: 0.7633 (mmm) REVERT: A 555 VAL cc_start: 0.7686 (t) cc_final: 0.7055 (m) REVERT: A 559 LYS cc_start: 0.7758 (ptmm) cc_final: 0.7325 (ptpt) REVERT: A 625 ARG cc_start: 0.7670 (ptt180) cc_final: 0.7265 (tpp80) REVERT: A 659 HIS cc_start: 0.7723 (m90) cc_final: 0.7172 (m90) REVERT: A 747 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7907 (ttt) REVERT: A 778 ASP cc_start: 0.8014 (t70) cc_final: 0.7684 (t0) REVERT: A 799 PHE cc_start: 0.5266 (OUTLIER) cc_final: 0.4916 (m-80) REVERT: A 816 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8207 (mp) REVERT: A 884 MET cc_start: 0.8001 (tpt) cc_final: 0.7747 (ttm) REVERT: A 890 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7816 (t0) REVERT: A 981 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7737 (tp) REVERT: A 999 LYS cc_start: 0.8169 (mmmm) cc_final: 0.7761 (mttt) REVERT: A 1053 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7876 (tm-30) REVERT: A 1330 ARG cc_start: 0.8254 (mmm160) cc_final: 0.7421 (mmt180) REVERT: A 1331 SER cc_start: 0.7942 (t) cc_final: 0.7689 (m) outliers start: 42 outliers final: 30 residues processed: 166 average time/residue: 0.0891 time to fit residues: 20.8836 Evaluate side-chains 167 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 55 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 163 HIS ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.160013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.123741 restraints weight = 11427.148| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.05 r_work: 0.3237 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9817 Z= 0.118 Angle : 0.513 7.471 13284 Z= 0.268 Chirality : 0.039 0.289 1510 Planarity : 0.003 0.047 1675 Dihedral : 7.913 78.589 1392 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.46 % Allowed : 26.99 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.25), residues: 1202 helix: 2.01 (0.19), residues: 748 sheet: -0.74 (0.61), residues: 79 loop : -1.69 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.018 0.001 TYR A 447 PHE 0.015 0.001 PHE A1048 TRP 0.010 0.001 TRP A 988 HIS 0.010 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 9817) covalent geometry : angle 0.51275 / 0.27 (13284) hydrogen bonds : bond 0.03769 / 2.53 ( 575) hydrogen bonds : angle 3.91442 / 2.84 ( 1692) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8395 (tp) cc_final: 0.8163 (tp) REVERT: A 104 MET cc_start: 0.8608 (tpt) cc_final: 0.8229 (mmm) REVERT: A 110 LEU cc_start: 0.7655 (tp) cc_final: 0.7376 (mt) REVERT: A 128 LYS cc_start: 0.7228 (mtmt) cc_final: 0.7013 (mtpp) REVERT: A 158 MET cc_start: 0.6762 (tpt) cc_final: 0.6189 (ttm) REVERT: A 192 ASN cc_start: 0.8841 (t0) cc_final: 0.8518 (t0) REVERT: A 251 LYS cc_start: 0.7988 (mmmm) cc_final: 0.7422 (pttm) REVERT: A 339 ILE cc_start: 0.8751 (mt) cc_final: 0.8306 (mt) REVERT: A 377 MET cc_start: 0.2035 (tpt) cc_final: 0.1351 (tpp) REVERT: A 381 ILE cc_start: 0.5639 (OUTLIER) cc_final: 0.5379 (tp) REVERT: A 413 ASP cc_start: 0.8375 (t0) cc_final: 0.7949 (m-30) REVERT: A 517 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7520 (mm-30) REVERT: A 544 GLN cc_start: 0.7955 (mp10) cc_final: 0.7559 (pm20) REVERT: A 554 MET cc_start: 0.7855 (ttt) cc_final: 0.7613 (mmm) REVERT: A 555 VAL cc_start: 0.7658 (t) cc_final: 0.7045 (m) REVERT: A 559 LYS cc_start: 0.7694 (ptmm) cc_final: 0.7268 (ptpt) REVERT: A 659 HIS cc_start: 0.7692 (m90) cc_final: 0.7160 (m90) REVERT: A 747 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8018 (ttm) REVERT: A 778 ASP cc_start: 0.8006 (t70) cc_final: 0.7701 (t0) REVERT: A 799 PHE cc_start: 0.5253 (OUTLIER) cc_final: 0.4906 (m-80) REVERT: A 816 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8212 (mp) REVERT: A 884 MET cc_start: 0.7930 (tpt) cc_final: 0.7697 (ttm) REVERT: A 890 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7820 (t0) REVERT: A 981 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7729 (tp) REVERT: A 999 LYS cc_start: 0.8169 (mmmm) cc_final: 0.7780 (mttt) REVERT: A 1053 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7870 (tm-30) REVERT: A 1330 ARG cc_start: 0.8268 (mmm160) cc_final: 0.7467 (mmt180) REVERT: A 1331 SER cc_start: 0.7973 (t) cc_final: 0.7711 (m) outliers start: 36 outliers final: 29 residues processed: 160 average time/residue: 0.0877 time to fit residues: 19.8198 Evaluate side-chains 164 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 0.0770 chunk 65 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.159981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123740 restraints weight = 11395.006| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.04 r_work: 0.3240 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9817 Z= 0.121 Angle : 0.516 7.507 13284 Z= 0.269 Chirality : 0.039 0.292 1510 Planarity : 0.003 0.047 1675 Dihedral : 7.730 77.444 1392 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.94 % Allowed : 26.32 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.25), residues: 1202 helix: 2.04 (0.19), residues: 748 sheet: -0.72 (0.61), residues: 79 loop : -1.69 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.018 0.001 TYR A 447 PHE 0.015 0.001 PHE A1048 TRP 0.010 0.001 TRP A 988 HIS 0.008 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9817) covalent geometry : angle 0.51622 / 0.27 (13284) hydrogen bonds : bond 0.03765 / 2.52 ( 575) hydrogen bonds : angle 3.91483 / 2.84 ( 1692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2213.23 seconds wall clock time: 38 minutes 46.94 seconds (2326.94 seconds total)