Starting phenix.real_space_refine on Tue Jul 29 21:57:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vgj_31971/07_2025/7vgj_31971.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vgj_31971/07_2025/7vgj_31971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vgj_31971/07_2025/7vgj_31971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vgj_31971/07_2025/7vgj_31971.map" model { file = "/net/cci-nas-00/data/ceres_data/7vgj_31971/07_2025/7vgj_31971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vgj_31971/07_2025/7vgj_31971.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 57 5.16 5 C 7413 2.51 5 N 1904 2.21 5 O 2085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11460 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8753 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 27, 'TRANS': 1056} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2653 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 25, 'TRANS': 304} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Classifications: {'peptide': 1} Time building chain proxies: 7.28, per 1000 atoms: 0.64 Number of scatterers: 11460 At special positions: 0 Unit cell: (100.287, 107.378, 172.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 1 15.00 O 2085 8.00 N 1904 7.00 C 7413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 105 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.5 seconds 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2672 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 10 sheets defined 44.8% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 106 through 116 removed outlier: 4.319A pdb=" N MET A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 132 Processing helix chain 'A' and resid 144 through 164 removed outlier: 3.732A pdb=" N VAL A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 151 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 removed outlier: 4.194A pdb=" N LYS A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.768A pdb=" N GLN A 248 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 331 through 367 removed outlier: 3.777A pdb=" N TYR A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 390 removed outlier: 3.821A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 removed outlier: 4.404A pdb=" N GLU A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 454 through 459 removed outlier: 3.925A pdb=" N THR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 519 removed outlier: 4.889A pdb=" N ILE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 534 Processing helix chain 'A' and resid 555 through 565 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 634 through 647 removed outlier: 4.114A pdb=" N GLU A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 645 " --> pdb=" O ASP A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 678 removed outlier: 4.089A pdb=" N LYS A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL A 678 " --> pdb=" O MET A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 692 removed outlier: 3.556A pdb=" N VAL A 690 " --> pdb=" O ALA A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 735 through 746 removed outlier: 3.614A pdb=" N ALA A 739 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 769 Processing helix chain 'A' and resid 803 through 811 Processing helix chain 'A' and resid 841 through 846 Processing helix chain 'A' and resid 848 through 859 Processing helix chain 'A' and resid 869 through 883 removed outlier: 3.682A pdb=" N ALA A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 900 removed outlier: 4.030A pdb=" N ASN A 899 " --> pdb=" O ASN A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 922 Processing helix chain 'A' and resid 931 through 936 Processing helix chain 'A' and resid 939 through 969 removed outlier: 4.082A pdb=" N PHE A 955 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR A 956 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN A 958 " --> pdb=" O PHE A 954 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N HIS A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 973 removed outlier: 3.878A pdb=" N GLY A 973 " --> pdb=" O PHE A 970 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 970 through 973' Processing helix chain 'A' and resid 981 through 986 removed outlier: 4.096A pdb=" N THR A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 992 Processing helix chain 'A' and resid 994 through 1004 Processing helix chain 'A' and resid 1008 through 1015 Processing helix chain 'A' and resid 1019 through 1025 removed outlier: 3.982A pdb=" N GLN A1023 " --> pdb=" O TYR A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1056 removed outlier: 3.768A pdb=" N LEU A1042 " --> pdb=" O LEU A1038 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A1043 " --> pdb=" O HIS A1039 " (cutoff:3.500A) Proline residue: A1051 - end of helix Processing helix chain 'A' and resid 1068 through 1073 Processing helix chain 'A' and resid 1073 through 1092 removed outlier: 4.244A pdb=" N ALA A1079 " --> pdb=" O THR A1075 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A1085 " --> pdb=" O VAL A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1117 Processing helix chain 'A' and resid 1119 through 1124 removed outlier: 3.895A pdb=" N HIS A1123 " --> pdb=" O SER A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1140 Processing helix chain 'A' and resid 1148 through 1171 Proline residue: A1159 - end of helix Processing helix chain 'A' and resid 1173 through 1181 removed outlier: 4.075A pdb=" N HIS A1181 " --> pdb=" O LYS A1177 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 62 removed outlier: 4.013A pdb=" N LEU B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Proline residue: B 55 - end of helix Processing helix chain 'B' and resid 64 through 77 removed outlier: 4.038A pdb=" N THR B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 134 through 139 removed outlier: 3.575A pdb=" N LYS B 139 " --> pdb=" O ARG B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 148 removed outlier: 3.715A pdb=" N GLY B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 155 removed outlier: 3.693A pdb=" N LEU B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 227 through 231 removed outlier: 3.978A pdb=" N LYS B 231 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.570A pdb=" N MET B 245 " --> pdb=" O PRO B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 265 Processing helix chain 'B' and resid 325 through 354 removed outlier: 3.915A pdb=" N GLY B 329 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 189 removed outlier: 4.089A pdb=" N GLU A 179 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 308 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 189 removed outlier: 4.089A pdb=" N GLU A 179 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 308 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 240 removed outlier: 4.140A pdb=" N VAL A 299 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 799 through 802 removed outlier: 5.690A pdb=" N LEU A 799 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N CYS A 866 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE A 801 " --> pdb=" O CYS A 866 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 863 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 451 " --> pdb=" O TRP A 729 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU A 731 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N SER A 453 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TYR A 450 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE A 891 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE A 452 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A 888 " --> pdb=" O ILE A 906 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 908 " --> pdb=" O THR A 888 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA A 890 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE A 910 " --> pdb=" O ALA A 890 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLY A 892 " --> pdb=" O ILE A 910 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 540 Processing sheet with id=AA7, first strand: chain 'A' and resid 569 through 570 removed outlier: 4.134A pdb=" N THR A 578 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE A 606 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE A 593 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N SER A 604 " --> pdb=" O ILE A 593 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 652 through 658 removed outlier: 5.791A pdb=" N TYR A 658 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A 700 " --> pdb=" O TYR A 658 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 81 through 82 removed outlier: 4.070A pdb=" N ILE B 81 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 315 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N TYR B 125 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU B 275 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU B 127 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG B 273 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 105 through 113 removed outlier: 4.014A pdb=" N CYS B 105 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG B 293 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 191 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR B 185 " --> pdb=" O THR B 299 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1200 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: 3.74 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1845 1.30 - 1.43: 3230 1.43 - 1.56: 6569 1.56 - 1.69: 2 1.69 - 1.81: 87 Bond restraints: 11733 Sorted by residual: bond pdb=" N LEU A 294 " pdb=" CA LEU A 294 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.23e-02 6.61e+03 8.38e+00 bond pdb=" C38 P5S A1301 " pdb=" O37 P5S A1301 " ideal model delta sigma weight residual 1.345 1.396 -0.051 2.00e-02 2.50e+03 6.60e+00 bond pdb=" N HIS A 510 " pdb=" CA HIS A 510 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.28e-02 6.10e+03 6.53e+00 bond pdb=" C17 P5S A1301 " pdb=" O19 P5S A1301 " ideal model delta sigma weight residual 1.351 1.401 -0.050 2.00e-02 2.50e+03 6.30e+00 bond pdb=" N ASP A 454 " pdb=" CA ASP A 454 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.22e-02 6.72e+03 6.11e+00 ... (remaining 11728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 15572 2.70 - 5.39: 271 5.39 - 8.09: 36 8.09 - 10.79: 9 10.79 - 13.49: 2 Bond angle restraints: 15890 Sorted by residual: angle pdb=" CA PRO B 90 " pdb=" N PRO B 90 " pdb=" CD PRO B 90 " ideal model delta sigma weight residual 112.00 105.18 6.82 1.40e+00 5.10e-01 2.37e+01 angle pdb=" O13 P5S A1301 " pdb=" P12 P5S A1301 " pdb=" O15 P5S A1301 " ideal model delta sigma weight residual 121.25 107.76 13.49 3.00e+00 1.11e-01 2.02e+01 angle pdb=" N PRO B 90 " pdb=" CD PRO B 90 " pdb=" CG PRO B 90 " ideal model delta sigma weight residual 103.20 96.59 6.61 1.50e+00 4.44e-01 1.94e+01 angle pdb=" N ASP A 289 " pdb=" CA ASP A 289 " pdb=" C ASP A 289 " ideal model delta sigma weight residual 108.19 113.31 -5.12 1.29e+00 6.01e-01 1.58e+01 angle pdb=" CA LEU A1125 " pdb=" CB LEU A1125 " pdb=" CG LEU A1125 " ideal model delta sigma weight residual 116.30 129.06 -12.76 3.50e+00 8.16e-02 1.33e+01 ... (remaining 15885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.81: 6817 33.81 - 67.61: 146 67.61 - 101.42: 22 101.42 - 135.22: 3 135.22 - 169.03: 3 Dihedral angle restraints: 6991 sinusoidal: 2845 harmonic: 4146 Sorted by residual: dihedral pdb=" CA ILE B 171 " pdb=" C ILE B 171 " pdb=" N ALA B 172 " pdb=" CA ALA B 172 " ideal model delta harmonic sigma weight residual 180.00 -152.28 -27.72 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA THR A 398 " pdb=" C THR A 398 " pdb=" N MET A 399 " pdb=" CA MET A 399 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLU A 649 " pdb=" C GLU A 649 " pdb=" N THR A 650 " pdb=" CA THR A 650 " ideal model delta harmonic sigma weight residual 180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 6988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1215 0.048 - 0.097: 438 0.097 - 0.145: 90 0.145 - 0.194: 11 0.194 - 0.242: 5 Chirality restraints: 1759 Sorted by residual: chirality pdb=" CB ILE A 181 " pdb=" CA ILE A 181 " pdb=" CG1 ILE A 181 " pdb=" CG2 ILE A 181 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE A 394 " pdb=" CA ILE A 394 " pdb=" CG1 ILE A 394 " pdb=" CG2 ILE A 394 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA GLU B 161 " pdb=" N GLU B 161 " pdb=" C GLU B 161 " pdb=" CB GLU B 161 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1756 not shown) Planarity restraints: 2010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 133 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.87e+00 pdb=" N PRO A 134 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 134 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 134 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 89 " 0.045 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO B 90 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 302 " -0.012 2.00e-02 2.50e+03 1.63e-02 5.31e+00 pdb=" CG TYR B 302 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 302 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 302 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR B 302 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 302 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 302 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 302 " 0.001 2.00e-02 2.50e+03 ... (remaining 2007 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 719 2.71 - 3.26: 13045 3.26 - 3.80: 18684 3.80 - 4.35: 23232 4.35 - 4.90: 36967 Nonbonded interactions: 92647 Sorted by model distance: nonbonded pdb=" NZ LYS A 238 " pdb=" O PHE A 239 " model vdw 2.160 3.120 nonbonded pdb=" O PRO B 290 " pdb=" OH TYR B 294 " model vdw 2.168 3.040 nonbonded pdb=" NZ LYS A 240 " pdb=" O ILE A 293 " model vdw 2.197 3.120 nonbonded pdb=" NZ LYS B 235 " pdb=" O PRO B 236 " model vdw 2.203 3.120 nonbonded pdb=" O TYR A 992 " pdb=" OG SER A1106 " model vdw 2.205 3.040 ... (remaining 92642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.500 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 0.007 0.079 11734 Z= 0.317 Angle : 0.917 13.487 15892 Z= 0.481 Chirality : 0.051 0.242 1759 Planarity : 0.005 0.070 2010 Dihedral : 16.170 169.027 4316 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 26.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.43 % Favored : 83.57 % Rotamer: Outliers : 0.48 % Allowed : 0.32 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.21), residues: 1406 helix: -1.32 (0.21), residues: 531 sheet: -2.05 (0.44), residues: 142 loop : -3.34 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 191 HIS 0.007 0.002 HIS A 535 PHE 0.019 0.002 PHE A 207 TYR 0.037 0.003 TYR B 302 ARG 0.012 0.001 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.16119 ( 424) hydrogen bonds : angle 7.88324 ( 1200) SS BOND : bond 0.00377 ( 1) SS BOND : angle 0.32632 ( 2) covalent geometry : bond 0.00704 (11733) covalent geometry : angle 0.91747 (15890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 1.237 Fit side-chains TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. REVERT: A 237 LEU cc_start: 0.8410 (tp) cc_final: 0.7599 (tp) REVERT: A 467 LYS cc_start: 0.8593 (tppt) cc_final: 0.8159 (tppp) REVERT: A 538 MET cc_start: 0.8515 (mpp) cc_final: 0.8051 (mpp) REVERT: A 875 MET cc_start: 0.8649 (tmm) cc_final: 0.8396 (tmm) REVERT: A 1113 ILE cc_start: 0.6186 (tp) cc_final: 0.5959 (tp) REVERT: B 163 TYR cc_start: 0.7418 (p90) cc_final: 0.6791 (p90) REVERT: B 314 ILE cc_start: 0.9068 (pt) cc_final: 0.8411 (pt) outliers start: 6 outliers final: 2 residues processed: 126 average time/residue: 0.1898 time to fit residues: 37.2214 Evaluate side-chains 104 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 692 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN A1061 GLN ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.096677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.068981 restraints weight = 40287.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.071113 restraints weight = 21138.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.072429 restraints weight = 14227.426| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11734 Z= 0.141 Angle : 0.717 10.632 15892 Z= 0.363 Chirality : 0.045 0.179 1759 Planarity : 0.004 0.044 2010 Dihedral : 11.756 169.176 1605 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 1.13 % Allowed : 9.26 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.22), residues: 1406 helix: -0.67 (0.22), residues: 555 sheet: -1.50 (0.47), residues: 132 loop : -3.12 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 191 HIS 0.006 0.001 HIS A 535 PHE 0.023 0.002 PHE A 853 TYR 0.022 0.002 TYR A 476 ARG 0.005 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.04808 ( 424) hydrogen bonds : angle 5.96968 ( 1200) SS BOND : bond 0.00306 ( 1) SS BOND : angle 0.35020 ( 2) covalent geometry : bond 0.00310 (11733) covalent geometry : angle 0.71687 (15890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it. REVERT: A 130 LEU cc_start: 0.8899 (tt) cc_final: 0.8638 (tt) REVERT: A 211 ASP cc_start: 0.7656 (m-30) cc_final: 0.7453 (m-30) REVERT: A 538 MET cc_start: 0.8170 (mpp) cc_final: 0.7581 (mpp) REVERT: A 720 LYS cc_start: 0.9123 (mtpt) cc_final: 0.8826 (mtmm) REVERT: A 747 GLU cc_start: 0.7756 (mp0) cc_final: 0.7476 (mp0) REVERT: B 163 TYR cc_start: 0.7534 (p90) cc_final: 0.6703 (p90) outliers start: 14 outliers final: 9 residues processed: 145 average time/residue: 0.1875 time to fit residues: 42.7557 Evaluate side-chains 125 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain B residue 342 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 37 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1118 HIS ** 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 = 0.3730 r_free = 0.3730 target = 0.095141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.067091 restraints weight = 41185.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.069070 restraints weight = 22220.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.070325 restraints weight = 15386.071| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11734 Z= 0.201 Angle : 0.713 9.033 15892 Z= 0.363 Chirality : 0.045 0.190 1759 Planarity : 0.004 0.041 2010 Dihedral : 11.456 167.656 1605 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.30 % Favored : 87.70 % Rotamer: Outliers : 2.01 % Allowed : 15.06 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.22), residues: 1406 helix: -0.57 (0.22), residues: 556 sheet: -1.46 (0.45), residues: 144 loop : -3.10 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 191 HIS 0.005 0.001 HIS A 510 PHE 0.026 0.002 PHE B 217 TYR 0.025 0.002 TYR A 476 ARG 0.004 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.04956 ( 424) hydrogen bonds : angle 5.88053 ( 1200) SS BOND : bond 0.00312 ( 1) SS BOND : angle 0.29728 ( 2) covalent geometry : bond 0.00459 (11733) covalent geometry : angle 0.71309 (15890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 1.197 Fit side-chains REVERT: A 130 LEU cc_start: 0.8914 (tt) cc_final: 0.8578 (tt) REVERT: A 467 LYS cc_start: 0.9208 (tppt) cc_final: 0.8941 (tppp) REVERT: A 538 MET cc_start: 0.8241 (mpp) cc_final: 0.7639 (mpp) REVERT: A 720 LYS cc_start: 0.9111 (mtpt) cc_final: 0.8797 (mtmm) REVERT: A 747 GLU cc_start: 0.7796 (mp0) cc_final: 0.7557 (mp0) REVERT: A 875 MET cc_start: 0.8682 (tmm) cc_final: 0.8361 (tmm) REVERT: B 163 TYR cc_start: 0.7966 (p90) cc_final: 0.7016 (p90) outliers start: 25 outliers final: 18 residues processed: 134 average time/residue: 0.1819 time to fit residues: 39.0760 Evaluate side-chains 131 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 72 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 117 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 45 optimal weight: 0.0670 chunk 48 optimal weight: 0.9990 chunk 92 optimal weight: 0.0770 chunk 111 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A 442 ASN A 474 GLN A 545 GLN A 917 GLN A 965 HIS ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.098581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.073182 restraints weight = 40588.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.073671 restraints weight = 23963.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.073803 restraints weight = 18405.845| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11734 Z= 0.112 Angle : 0.651 10.227 15892 Z= 0.325 Chirality : 0.043 0.160 1759 Planarity : 0.004 0.041 2010 Dihedral : 10.565 164.688 1602 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 1.77 % Allowed : 17.55 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.22), residues: 1406 helix: -0.25 (0.22), residues: 550 sheet: -1.02 (0.47), residues: 135 loop : -2.88 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 191 HIS 0.005 0.001 HIS A 510 PHE 0.017 0.001 PHE B 217 TYR 0.039 0.002 TYR A 476 ARG 0.004 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 424) hydrogen bonds : angle 5.36881 ( 1200) SS BOND : bond 0.00343 ( 1) SS BOND : angle 0.27676 ( 2) covalent geometry : bond 0.00234 (11733) covalent geometry : angle 0.65087 (15890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8795 (tt) cc_final: 0.8447 (tt) REVERT: A 538 MET cc_start: 0.8072 (mpp) cc_final: 0.7522 (mpp) REVERT: A 747 GLU cc_start: 0.7755 (mp0) cc_final: 0.7506 (mp0) REVERT: A 769 MET cc_start: 0.7344 (ppp) cc_final: 0.5245 (ptt) REVERT: B 40 ARG cc_start: 0.8009 (ptp90) cc_final: 0.7761 (ptt90) REVERT: B 56 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7649 (mp) REVERT: B 163 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7089 (p90) outliers start: 22 outliers final: 10 residues processed: 163 average time/residue: 0.1922 time to fit residues: 48.5956 Evaluate side-chains 141 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 304 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 88 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 127 optimal weight: 0.0270 chunk 12 optimal weight: 0.8980 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 GLN ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.099007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.073273 restraints weight = 40270.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.073970 restraints weight = 26648.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.074609 restraints weight = 19259.154| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11734 Z= 0.111 Angle : 0.660 10.098 15892 Z= 0.327 Chirality : 0.042 0.156 1759 Planarity : 0.004 0.071 2010 Dihedral : 10.088 156.414 1602 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 1.85 % Allowed : 19.73 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.23), residues: 1406 helix: -0.02 (0.23), residues: 537 sheet: -0.97 (0.46), residues: 137 loop : -2.64 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 191 HIS 0.005 0.001 HIS A 510 PHE 0.030 0.001 PHE A 124 TYR 0.036 0.001 TYR A 476 ARG 0.003 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 424) hydrogen bonds : angle 5.18535 ( 1200) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.99109 ( 2) covalent geometry : bond 0.00238 (11733) covalent geometry : angle 0.65994 (15890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8780 (tt) cc_final: 0.8420 (tt) REVERT: A 538 MET cc_start: 0.8226 (mpp) cc_final: 0.7709 (mpp) REVERT: A 747 GLU cc_start: 0.7728 (mp0) cc_final: 0.7525 (mp0) REVERT: A 769 MET cc_start: 0.7322 (ppp) cc_final: 0.5177 (ptm) REVERT: A 875 MET cc_start: 0.8606 (ppp) cc_final: 0.8355 (ppp) REVERT: A 879 LEU cc_start: 0.9035 (mt) cc_final: 0.8739 (tp) REVERT: B 56 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7553 (mp) REVERT: B 163 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.7036 (p90) outliers start: 23 outliers final: 14 residues processed: 158 average time/residue: 0.1815 time to fit residues: 45.5437 Evaluate side-chains 145 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 12 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 133 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.096150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.068195 restraints weight = 41074.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.070227 restraints weight = 22303.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.071494 restraints weight = 15305.618| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11734 Z= 0.192 Angle : 0.715 11.934 15892 Z= 0.356 Chirality : 0.045 0.171 1759 Planarity : 0.004 0.040 2010 Dihedral : 10.003 144.982 1602 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 2.82 % Allowed : 21.34 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.23), residues: 1406 helix: -0.18 (0.22), residues: 556 sheet: -1.08 (0.45), residues: 148 loop : -2.76 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 191 HIS 0.005 0.001 HIS A 510 PHE 0.025 0.002 PHE A 124 TYR 0.038 0.002 TYR A 476 ARG 0.003 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 424) hydrogen bonds : angle 5.38882 ( 1200) SS BOND : bond 0.00337 ( 1) SS BOND : angle 0.36718 ( 2) covalent geometry : bond 0.00440 (11733) covalent geometry : angle 0.71540 (15890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8905 (tt) cc_final: 0.8518 (tt) REVERT: A 466 PHE cc_start: 0.7563 (t80) cc_final: 0.7111 (t80) REVERT: A 538 MET cc_start: 0.8275 (mpp) cc_final: 0.7655 (mpp) REVERT: A 747 GLU cc_start: 0.7919 (mp0) cc_final: 0.7633 (mp0) REVERT: A 769 MET cc_start: 0.7392 (ppp) cc_final: 0.5269 (ptt) REVERT: B 56 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7580 (mp) REVERT: B 163 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7282 (p90) outliers start: 35 outliers final: 27 residues processed: 146 average time/residue: 0.1899 time to fit residues: 45.0790 Evaluate side-chains 154 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 342 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 67 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 127 optimal weight: 0.0070 chunk 20 optimal weight: 0.0470 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.099105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.074400 restraints weight = 40929.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074236 restraints weight = 24649.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074780 restraints weight = 20608.306| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11734 Z= 0.113 Angle : 0.669 15.008 15892 Z= 0.327 Chirality : 0.042 0.153 1759 Planarity : 0.004 0.037 2010 Dihedral : 9.575 142.066 1602 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 1.93 % Allowed : 22.46 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.23), residues: 1406 helix: 0.08 (0.23), residues: 544 sheet: -1.03 (0.45), residues: 142 loop : -2.54 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 805 HIS 0.006 0.001 HIS A 630 PHE 0.021 0.001 PHE B 340 TYR 0.035 0.001 TYR A 476 ARG 0.003 0.000 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 424) hydrogen bonds : angle 5.16703 ( 1200) SS BOND : bond 0.00358 ( 1) SS BOND : angle 0.39770 ( 2) covalent geometry : bond 0.00236 (11733) covalent geometry : angle 0.66931 (15890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8787 (tt) cc_final: 0.8389 (tt) REVERT: A 466 PHE cc_start: 0.7620 (t80) cc_final: 0.7167 (t80) REVERT: A 538 MET cc_start: 0.8158 (mpp) cc_final: 0.7645 (mpp) REVERT: A 747 GLU cc_start: 0.7753 (mp0) cc_final: 0.7484 (mp0) REVERT: A 769 MET cc_start: 0.7356 (ppp) cc_final: 0.5258 (ptt) REVERT: A 879 LEU cc_start: 0.9230 (mt) cc_final: 0.8703 (tp) REVERT: B 56 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7634 (mp) REVERT: B 163 TYR cc_start: 0.7801 (OUTLIER) cc_final: 0.7005 (p90) outliers start: 24 outliers final: 20 residues processed: 161 average time/residue: 0.1832 time to fit residues: 47.0261 Evaluate side-chains 160 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 84 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 48 optimal weight: 0.0270 chunk 59 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.096883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.071822 restraints weight = 41411.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.071985 restraints weight = 30546.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.072258 restraints weight = 22119.734| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11734 Z= 0.170 Angle : 0.700 13.937 15892 Z= 0.343 Chirality : 0.043 0.149 1759 Planarity : 0.004 0.039 2010 Dihedral : 9.455 133.940 1602 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 2.82 % Allowed : 22.22 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.23), residues: 1406 helix: -0.01 (0.23), residues: 554 sheet: -1.17 (0.44), residues: 155 loop : -2.62 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 191 HIS 0.004 0.001 HIS A 510 PHE 0.020 0.001 PHE B 217 TYR 0.038 0.002 TYR A 476 ARG 0.003 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 424) hydrogen bonds : angle 5.30503 ( 1200) SS BOND : bond 0.00325 ( 1) SS BOND : angle 0.27719 ( 2) covalent geometry : bond 0.00393 (11733) covalent geometry : angle 0.70022 (15890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: A 466 PHE cc_start: 0.7565 (t80) cc_final: 0.7128 (t80) REVERT: A 538 MET cc_start: 0.8119 (mpp) cc_final: 0.7709 (mpp) REVERT: A 747 GLU cc_start: 0.7831 (mp0) cc_final: 0.7559 (mp0) REVERT: A 769 MET cc_start: 0.7083 (ppp) cc_final: 0.4553 (ptm) REVERT: B 56 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7710 (mp) REVERT: B 163 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7141 (p90) outliers start: 35 outliers final: 29 residues processed: 154 average time/residue: 0.1724 time to fit residues: 43.1300 Evaluate side-chains 160 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 342 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 57 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 30.0000 chunk 13 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.097317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.072542 restraints weight = 41203.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.071672 restraints weight = 30125.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.072002 restraints weight = 23302.641| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11734 Z= 0.145 Angle : 0.699 14.415 15892 Z= 0.339 Chirality : 0.043 0.149 1759 Planarity : 0.004 0.039 2010 Dihedral : 9.365 131.912 1602 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 2.82 % Allowed : 22.38 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.23), residues: 1406 helix: 0.08 (0.23), residues: 544 sheet: -1.19 (0.44), residues: 152 loop : -2.52 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 191 HIS 0.004 0.001 HIS A 510 PHE 0.024 0.001 PHE B 340 TYR 0.034 0.002 TYR A 476 ARG 0.002 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 424) hydrogen bonds : angle 5.30139 ( 1200) SS BOND : bond 0.00309 ( 1) SS BOND : angle 0.28613 ( 2) covalent geometry : bond 0.00334 (11733) covalent geometry : angle 0.69912 (15890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8732 (tt) cc_final: 0.8486 (tt) REVERT: A 466 PHE cc_start: 0.7571 (t80) cc_final: 0.7110 (t80) REVERT: A 538 MET cc_start: 0.8209 (mpp) cc_final: 0.7661 (mpp) REVERT: A 747 GLU cc_start: 0.7874 (mp0) cc_final: 0.7565 (mp0) REVERT: A 769 MET cc_start: 0.6957 (ppp) cc_final: 0.4508 (ptm) REVERT: B 56 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7706 (mp) REVERT: B 163 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.7111 (p90) outliers start: 35 outliers final: 30 residues processed: 153 average time/residue: 0.1820 time to fit residues: 44.2657 Evaluate side-chains 161 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 49 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 129 optimal weight: 0.0000 chunk 51 optimal weight: 30.0000 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 92 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 overall best weight: 2.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.097673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.072456 restraints weight = 41096.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.072463 restraints weight = 27221.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.073086 restraints weight = 20086.025| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11734 Z= 0.134 Angle : 0.705 14.598 15892 Z= 0.340 Chirality : 0.043 0.153 1759 Planarity : 0.004 0.039 2010 Dihedral : 9.189 126.690 1602 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 2.82 % Allowed : 22.46 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.23), residues: 1406 helix: 0.12 (0.23), residues: 545 sheet: -1.18 (0.43), residues: 157 loop : -2.45 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 191 HIS 0.004 0.001 HIS A 510 PHE 0.017 0.001 PHE B 217 TYR 0.032 0.002 TYR A 476 ARG 0.002 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 424) hydrogen bonds : angle 5.24947 ( 1200) SS BOND : bond 0.00312 ( 1) SS BOND : angle 0.31866 ( 2) covalent geometry : bond 0.00307 (11733) covalent geometry : angle 0.70518 (15890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8687 (tt) cc_final: 0.8464 (tt) REVERT: A 412 ARG cc_start: 0.7813 (mtt-85) cc_final: 0.7560 (mtt-85) REVERT: A 466 PHE cc_start: 0.7528 (t80) cc_final: 0.7096 (t80) REVERT: A 538 MET cc_start: 0.8103 (mpp) cc_final: 0.7669 (mpp) REVERT: A 747 GLU cc_start: 0.7813 (mp0) cc_final: 0.7504 (mp0) REVERT: A 769 MET cc_start: 0.6955 (ppp) cc_final: 0.4486 (ptm) REVERT: B 56 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7660 (mp) REVERT: B 163 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.7061 (p90) REVERT: B 228 GLU cc_start: 0.7383 (pm20) cc_final: 0.7172 (pm20) outliers start: 35 outliers final: 29 residues processed: 155 average time/residue: 0.1928 time to fit residues: 47.4717 Evaluate side-chains 160 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 1 optimal weight: 0.0870 chunk 27 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 97 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.098827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.074598 restraints weight = 40632.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074095 restraints weight = 23118.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.074028 restraints weight = 20985.839| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11734 Z= 0.116 Angle : 0.698 14.982 15892 Z= 0.334 Chirality : 0.042 0.151 1759 Planarity : 0.004 0.037 2010 Dihedral : 9.052 125.952 1602 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 2.42 % Allowed : 22.79 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.23), residues: 1406 helix: 0.21 (0.23), residues: 547 sheet: -1.08 (0.43), residues: 157 loop : -2.39 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.004 0.001 HIS A 535 PHE 0.023 0.001 PHE B 340 TYR 0.028 0.001 TYR A 476 ARG 0.001 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 424) hydrogen bonds : angle 5.13699 ( 1200) SS BOND : bond 0.00295 ( 1) SS BOND : angle 0.31094 ( 2) covalent geometry : bond 0.00258 (11733) covalent geometry : angle 0.69805 (15890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3341.35 seconds wall clock time: 59 minutes 3.54 seconds (3543.54 seconds total)