Starting phenix.real_space_refine on Fri Jul 3 04:05:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8v_42028/07_2026/8u8v_42028.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8v_42028/07_2026/8u8v_42028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u8v_42028/07_2026/8u8v_42028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8v_42028/07_2026/8u8v_42028.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u8v_42028/07_2026/8u8v_42028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8v_42028/07_2026/8u8v_42028.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 64 5.49 5 Mg 1 5.21 5 S 58 5.16 5 C 7446 2.51 5 N 2108 2.21 5 O 2279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11956 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1617 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1528 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'PHE:plan': 2, 'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "E" Number of atoms: 7518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7518 Classifications: {'peptide': 990} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 68, 'TRANS': 921} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 467 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 10, 'HIS:plan': 4, 'ARG:plan': 17, 'PHE:plan': 2, 'GLU:plan': 14, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 269 Chain: "N" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 453 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "R" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'APC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.87, per 1000 atoms: 0.24 Number of scatterers: 11956 At special positions: 0 Unit cell: (105.165, 99.18, 129.105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 64 15.00 Mg 1 11.99 O 2279 8.00 N 2108 7.00 C 7446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 695.5 milliseconds 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 10 sheets defined 56.3% alpha, 6.8% beta 20 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 149 through 155 removed outlier: 4.129A pdb=" N LYS A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 4.028A pdb=" N LEU A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 223 removed outlier: 4.217A pdb=" N LYS A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 Processing helix chain 'A' and resid 264 through 269 removed outlier: 3.581A pdb=" N ASP A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 296 through 305 removed outlier: 3.533A pdb=" N VAL A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 335 Processing helix chain 'A' and resid 341 through 354 removed outlier: 3.919A pdb=" N LEU A 345 " --> pdb=" O TYR A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 removed outlier: 3.514A pdb=" N LEU B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 166 removed outlier: 3.597A pdb=" N LEU B 164 " --> pdb=" O GLU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.574A pdb=" N TYR B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 262 removed outlier: 3.540A pdb=" N LEU B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 286 Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.947A pdb=" N VAL B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 330 Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.616A pdb=" N GLU B 339 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 353 removed outlier: 4.171A pdb=" N LEU B 345 " --> pdb=" O TYR B 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 236 removed outlier: 3.688A pdb=" N LEU E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 245 through 252 Processing helix chain 'E' and resid 253 through 257 removed outlier: 4.316A pdb=" N LYS E 257 " --> pdb=" O GLN E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 274 removed outlier: 3.975A pdb=" N GLN E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 291 Processing helix chain 'E' and resid 297 through 307 removed outlier: 3.983A pdb=" N GLY E 307 " --> pdb=" O LEU E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 325 Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 340 through 353 Processing helix chain 'E' and resid 392 through 409 removed outlier: 3.525A pdb=" N LEU E 396 " --> pdb=" O PRO E 392 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA E 409 " --> pdb=" O HIS E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 459 removed outlier: 3.631A pdb=" N ARG E 458 " --> pdb=" O ASN E 454 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU E 459 " --> pdb=" O ARG E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 473 removed outlier: 3.913A pdb=" N LEU E 471 " --> pdb=" O LEU E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 489 removed outlier: 3.765A pdb=" N GLN E 488 " --> pdb=" O LEU E 484 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA E 489 " --> pdb=" O GLN E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 520 removed outlier: 3.608A pdb=" N VAL E 514 " --> pdb=" O SER E 510 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER E 520 " --> pdb=" O ARG E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 534 removed outlier: 3.725A pdb=" N ALA E 525 " --> pdb=" O GLY E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 537 No H-bonds generated for 'chain 'E' and resid 535 through 537' Processing helix chain 'E' and resid 548 through 555 Processing helix chain 'E' and resid 568 through 586 removed outlier: 3.771A pdb=" N GLU E 574 " --> pdb=" O PRO E 570 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU E 575 " --> pdb=" O VAL E 571 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY E 576 " --> pdb=" O GLN E 572 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL E 584 " --> pdb=" O ALA E 580 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN E 585 " --> pdb=" O GLU E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 634 removed outlier: 3.946A pdb=" N ALA E 634 " --> pdb=" O LEU E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 644 through 646 No H-bonds generated for 'chain 'E' and resid 644 through 646' Processing helix chain 'E' and resid 678 through 687 Processing helix chain 'E' and resid 688 through 691 Processing helix chain 'E' and resid 692 through 704 removed outlier: 3.716A pdb=" N ALA E 698 " --> pdb=" O GLY E 694 " (cutoff:3.500A) Processing helix chain 'E' and resid 710 through 723 removed outlier: 3.984A pdb=" N LEU E 714 " --> pdb=" O ASN E 710 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA E 723 " --> pdb=" O GLN E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 730 removed outlier: 3.626A pdb=" N GLY E 730 " --> pdb=" O PRO E 727 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 738 Processing helix chain 'E' and resid 751 through 763 removed outlier: 3.622A pdb=" N LYS E 755 " --> pdb=" O ALA E 751 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA E 756 " --> pdb=" O PRO E 752 " (cutoff:3.500A) Processing helix chain 'E' and resid 764 through 789 removed outlier: 3.686A pdb=" N VAL E 768 " --> pdb=" O HIS E 764 " (cutoff:3.500A) Processing helix chain 'E' and resid 818 through 824 Processing helix chain 'E' and resid 837 through 850 Processing helix chain 'E' and resid 856 through 865 removed outlier: 3.625A pdb=" N ALA E 864 " --> pdb=" O ARG E 860 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU E 865 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing helix chain 'E' and resid 867 through 877 Processing helix chain 'E' and resid 890 through 906 Processing helix chain 'E' and resid 909 through 912 Processing helix chain 'E' and resid 925 through 932 removed outlier: 3.853A pdb=" N TYR E 931 " --> pdb=" O GLY E 927 " (cutoff:3.500A) Processing helix chain 'E' and resid 954 through 969 removed outlier: 3.613A pdb=" N ALA E 960 " --> pdb=" O TYR E 956 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA E 961 " --> pdb=" O SER E 957 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN E 962 " --> pdb=" O GLY E 958 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE E 966 " --> pdb=" O GLN E 962 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ARG E 967 " --> pdb=" O VAL E 963 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG E 968 " --> pdb=" O GLU E 964 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN E 969 " --> pdb=" O VAL E 965 " (cutoff:3.500A) Processing helix chain 'E' and resid 975 through 982 removed outlier: 3.604A pdb=" N LEU E 981 " --> pdb=" O VAL E 977 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU E 982 " --> pdb=" O ALA E 978 " (cutoff:3.500A) Processing helix chain 'E' and resid 986 through 997 removed outlier: 3.957A pdb=" N VAL E 990 " --> pdb=" O THR E 986 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN E 992 " --> pdb=" O LYS E 988 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N THR E 993 " --> pdb=" O VAL E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 1002 through 1017 removed outlier: 3.748A pdb=" N LYS E1012 " --> pdb=" O LEU E1008 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG E1013 " --> pdb=" O GLN E1009 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU E1016 " --> pdb=" O LYS E1012 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU E1017 " --> pdb=" O ARG E1013 " (cutoff:3.500A) Processing helix chain 'E' and resid 1025 through 1034 Processing helix chain 'E' and resid 1036 through 1044 Processing helix chain 'E' and resid 1047 through 1064 removed outlier: 3.572A pdb=" N MET E1064 " --> pdb=" O LEU E1060 " (cutoff:3.500A) Processing helix chain 'E' and resid 1111 through 1117 Processing helix chain 'E' and resid 1118 through 1141 removed outlier: 3.740A pdb=" N ILE E1124 " --> pdb=" O PRO E1120 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS E1125 " --> pdb=" O PRO E1121 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER E1126 " --> pdb=" O ASN E1122 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU E1127 " --> pdb=" O PHE E1123 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER E1129 " --> pdb=" O HIS E1125 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG E1141 " --> pdb=" O LEU E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1159 through 1176 removed outlier: 4.173A pdb=" N MET E1163 " --> pdb=" O ASP E1159 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG E1168 " --> pdb=" O ASN E1164 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL E1172 " --> pdb=" O ARG E1168 " (cutoff:3.500A) Processing helix chain 'E' and resid 1179 through 1192 Processing helix chain 'E' and resid 1197 through 1210 removed outlier: 3.617A pdb=" N ALA E1201 " --> pdb=" O LYS E1197 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA E1210 " --> pdb=" O GLU E1206 " (cutoff:3.500A) Processing helix chain 'E' and resid 1221 through 1225 removed outlier: 3.633A pdb=" N ARG E1224 " --> pdb=" O GLN E1221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 197 removed outlier: 5.820A pdb=" N PHE A 175 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 191 through 196 removed outlier: 4.171A pdb=" N ASP B 193 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 170 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 232 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE B 175 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR B 229 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N MET B 276 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 231 " --> pdb=" O MET B 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 411 through 415 Processing sheet with id=AA4, first strand: chain 'E' and resid 495 through 496 Processing sheet with id=AA5, first strand: chain 'E' and resid 588 through 589 Processing sheet with id=AA6, first strand: chain 'E' and resid 793 through 795 Processing sheet with id=AA7, first strand: chain 'E' and resid 798 through 800 Processing sheet with id=AA8, first strand: chain 'E' and resid 831 through 832 Processing sheet with id=AA9, first strand: chain 'E' and resid 919 through 922 Processing sheet with id=AB1, first strand: chain 'E' and resid 1069 through 1071 514 hydrogen bonds defined for protein. 1488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2706 1.33 - 1.46: 2974 1.46 - 1.58: 6463 1.58 - 1.70: 121 1.70 - 1.82: 95 Bond restraints: 12359 Sorted by residual: bond pdb=" N GLN E 953 " pdb=" CA GLN E 953 " ideal model delta sigma weight residual 1.456 1.505 -0.049 1.23e-02 6.61e+03 1.58e+01 bond pdb=" C3' DA T 13 " pdb=" C2' DA T 13 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 bond pdb=" N VAL E1033 " pdb=" CA VAL E1033 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.30e+01 bond pdb=" N ILE E 985 " pdb=" CA ILE E 985 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.19e-02 7.06e+03 1.29e+01 bond pdb=" C1' DT T 10 " pdb=" N1 DT T 10 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.13e+01 ... (remaining 12354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 16506 2.27 - 4.54: 472 4.54 - 6.81: 86 6.81 - 9.09: 20 9.09 - 11.36: 4 Bond angle restraints: 17088 Sorted by residual: angle pdb=" N THR E1047 " pdb=" CA THR E1047 " pdb=" C THR E1047 " ideal model delta sigma weight residual 113.41 102.51 10.90 1.22e+00 6.72e-01 7.98e+01 angle pdb=" N ALA E 971 " pdb=" CA ALA E 971 " pdb=" C ALA E 971 " ideal model delta sigma weight residual 112.87 104.48 8.39 1.20e+00 6.94e-01 4.89e+01 angle pdb=" N PRO E 948 " pdb=" CA PRO E 948 " pdb=" C PRO E 948 " ideal model delta sigma weight residual 111.14 120.70 -9.56 1.56e+00 4.11e-01 3.75e+01 angle pdb=" N LYS E1038 " pdb=" CA LYS E1038 " pdb=" C LYS E1038 " ideal model delta sigma weight residual 111.28 105.07 6.21 1.09e+00 8.42e-01 3.25e+01 angle pdb=" N GLN E1022 " pdb=" CA GLN E1022 " pdb=" C GLN E1022 " ideal model delta sigma weight residual 109.54 101.82 7.72 1.37e+00 5.33e-01 3.18e+01 ... (remaining 17083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.12: 6416 20.12 - 40.25: 590 40.25 - 60.37: 243 60.37 - 80.50: 43 80.50 - 100.62: 5 Dihedral angle restraints: 7297 sinusoidal: 3210 harmonic: 4087 Sorted by residual: dihedral pdb=" CA SER E1148 " pdb=" C SER E1148 " pdb=" N VAL E1149 " pdb=" CA VAL E1149 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA LEU E 934 " pdb=" C LEU E 934 " pdb=" N GLY E 935 " pdb=" CA GLY E 935 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TRP B 200 " pdb=" C TRP B 200 " pdb=" N SER B 201 " pdb=" CA SER B 201 " ideal model delta harmonic sigma weight residual 180.00 162.18 17.82 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 7294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1906 0.129 - 0.257: 47 0.257 - 0.386: 0 0.386 - 0.514: 5 0.514 - 0.643: 12 Chirality restraints: 1970 Sorted by residual: chirality pdb=" P DA N -24 " pdb=" OP1 DA N -24 " pdb=" OP2 DA N -24 " pdb=" O5' DA N -24 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P DG T -12 " pdb=" OP1 DG T -12 " pdb=" OP2 DG T -12 " pdb=" O5' DG T -12 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DC T -9 " pdb=" OP1 DC T -9 " pdb=" OP2 DC T -9 " pdb=" O5' DC T -9 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.54 2.00e-01 2.50e+01 7.37e+00 ... (remaining 1967 not shown) Planarity restraints: 1966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 949 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" C SER E 949 " -0.051 2.00e-02 2.50e+03 pdb=" O SER E 949 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP E 950 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP E 567 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO E 568 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO E 568 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 568 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 543 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO E 544 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO E 544 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 544 " -0.029 5.00e-02 4.00e+02 ... (remaining 1963 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 145 2.65 - 3.22: 10239 3.22 - 3.78: 18200 3.78 - 4.34: 23249 4.34 - 4.90: 37923 Nonbonded interactions: 89756 Sorted by model distance: nonbonded pdb=" OD2 ASP E1151 " pdb="MG MG E1302 " model vdw 2.092 2.170 nonbonded pdb=" O2A APC E1301 " pdb="MG MG E1302 " model vdw 2.147 2.170 nonbonded pdb=" O GLY E 923 " pdb="MG MG E1302 " model vdw 2.177 2.170 nonbonded pdb=" OG SER B 172 " pdb=" OG SER B 343 " model vdw 2.263 3.040 nonbonded pdb=" NE2 GLN E 766 " pdb=" OP1 DC T 12 " model vdw 2.281 3.120 ... (remaining 89751 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 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 149 through 150 and (name N or name CA or name C or name \ O or name CB )) or resid 151 through 152 or (resid 153 and (name N or name CA or \ name C or name O or name CB )) or resid 154 through 155 or (resid 156 and (name \ N or name CA or name C or name O or name CB )) or resid 157 through 164 or (res \ id 165 through 166 and (name N or name CA or name C or name O or name CB )) or r \ esid 167 through 178 or (resid 179 and (name N or name CA or name C or name O or \ name CB )) or resid 180 through 185 or (resid 186 through 188 and (name N or na \ me CA or name C or name O or name CB )) or resid 189 through 197 or (resid 198 t \ hrough 199 and (name N or name CA or name C or name O or name CB )) or resid 200 \ through 262 or (resid 263 and (name N or name CA or name C or name O or name CB \ )) or resid 264 through 282 or (resid 283 and (name N or name CA or name C or n \ ame O or name CB )) or resid 284 through 285 or (resid 286 and (name N or name C \ A or name C or name O or name CB )) or resid 287 or (resid 288 and (name N or na \ me CA or name C or name O or name CB )) or resid 289 through 301 or (resid 302 a \ nd (name N or name CA or name C or name O or name CB )) or resid 303 through 320 \ or (resid 321 and (name N or name CA or name C or name O or name CB )) or resid \ 322 through 325 or (resid 326 through 327 and (name N or name CA or name C or n \ ame O or name CB )) or resid 328 or (resid 329 through 330 and (name N or name C \ A or name C or name O or name CB )) or resid 331 or (resid 332 through 334 and ( \ name N or name CA or name C or name O or name CB )) or resid 335 through 340 or \ (resid 341 and (name N or name CA or name C or name O or name CB )) or resid 342 \ through 351 or (resid 352 and (name N or name CA or name C or name O or name CB \ )) or resid 353 through 355)) selection = (chain 'B' and (resid 149 through 160 or (resid 161 and (name N or name CA or na \ me C or name O or name CB )) or resid 162 through 221 or (resid 222 and (name N \ or name CA or name C or name O or name CB )) or resid 223 through 224 or (resid \ 225 through 226 and (name N or name CA or name C or name O or name CB )) or resi \ d 227 through 238 or (resid 239 and (name N or name CA or name C or name O or na \ me CB )) or resid 240 through 303 or (resid 304 and (name N or name CA or name C \ or name O or name CB )) or resid 305 or (resid 313 and (name N or name CA or na \ me C or name O or name CB )) or resid 314 through 332 or (resid 333 through 334 \ and (name N or name CA or name C or name O or name CB )) or resid 335 through 35 \ 5)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.330 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:10.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5401 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 : 0.005 0.049 12359 Z= 0.369 Angle : 0.907 11.358 17088 Z= 0.584 Chirality : 0.071 0.643 1970 Planarity : 0.006 0.066 1966 Dihedral : 18.505 100.622 4633 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.46 % Allowed : 3.47 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.21), residues: 1380 helix: 0.04 (0.19), residues: 699 sheet: -1.07 (0.57), residues: 83 loop : -1.91 (0.22), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1007 TYR 0.026 0.002 TYR E 956 PHE 0.021 0.002 PHE E 802 TRP 0.017 0.001 TRP A 182 HIS 0.006 0.001 HIS E1052 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.37 (12359) covalent geometry : angle 0.90725 / 0.58 (17088) hydrogen bonds : bond 0.19721 / 12.88 ( 568) hydrogen bonds : angle 6.48521 / 4.76 ( 1596) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 219 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 GLU cc_start: 0.7654 (mp0) cc_final: 0.7434 (mp0) REVERT: B 164 LEU cc_start: 0.7472 (mt) cc_final: 0.7206 (mp) REVERT: B 189 LEU cc_start: 0.6657 (tt) cc_final: 0.6134 (mm) REVERT: B 203 MET cc_start: 0.7285 (mmm) cc_final: 0.6927 (mmt) REVERT: B 217 SER cc_start: 0.6714 (t) cc_final: 0.6356 (m) REVERT: B 272 GLN cc_start: 0.7959 (tt0) cc_final: 0.7694 (tt0) REVERT: E 263 MET cc_start: 0.2526 (ptp) cc_final: 0.0898 (tpp) REVERT: E 372 LYS cc_start: 0.7187 (mmmt) cc_final: 0.6800 (mmmt) REVERT: E 406 MET cc_start: 0.6500 (tmm) cc_final: 0.6104 (ttt) REVERT: E 465 PHE cc_start: 0.6174 (t80) cc_final: 0.5924 (t80) REVERT: E 503 GLU cc_start: 0.5624 (mm-30) cc_final: 0.5390 (mm-30) REVERT: E 539 SER cc_start: 0.7613 (t) cc_final: 0.7170 (p) REVERT: E 585 GLN cc_start: 0.6615 (tm-30) cc_final: 0.5917 (pp30) REVERT: E 588 GLN cc_start: 0.6468 (mt0) cc_final: 0.6215 (mt0) REVERT: E 611 SER cc_start: 0.6908 (t) cc_final: 0.6640 (p) REVERT: E 615 VAL cc_start: 0.7553 (t) cc_final: 0.7333 (t) REVERT: E 640 THR cc_start: 0.7010 (t) cc_final: 0.6760 (m) REVERT: E 682 GLU cc_start: 0.5979 (tp30) cc_final: 0.5691 (tp30) REVERT: E 772 MET cc_start: 0.6858 (mtp) cc_final: 0.6640 (mtm) REVERT: E 831 ARG cc_start: 0.7298 (mmt-90) cc_final: 0.7046 (mmm-85) REVERT: E 882 ARG cc_start: 0.7081 (mtm180) cc_final: 0.6777 (mtm-85) outliers start: 5 outliers final: 2 residues processed: 222 average time/residue: 0.6070 time to fit residues: 145.5150 Evaluate side-chains 179 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 955 VAL Chi-restraints excluded: chain E residue 1031 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 GLN A 346 GLN ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 HIS E 836 HIS E 893 GLN E 903 ASN E 945 ASN E1051 GLN ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1117 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.196390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.166427 restraints weight = 16207.498| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 1.70 r_work: 0.3954 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12359 Z= 0.157 Angle : 0.657 11.168 17088 Z= 0.349 Chirality : 0.044 0.232 1970 Planarity : 0.006 0.078 1966 Dihedral : 19.573 103.372 2235 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.74 % Allowed : 11.52 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.22), residues: 1380 helix: 0.72 (0.20), residues: 697 sheet: -0.54 (0.54), residues: 98 loop : -1.75 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 507 TYR 0.019 0.002 TYR E 468 PHE 0.016 0.002 PHE E 497 TRP 0.012 0.001 TRP A 182 HIS 0.004 0.001 HIS E1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (12359) covalent geometry : angle 0.65664 / 0.35 (17088) hydrogen bonds : bond 0.05523 / 3.59 ( 568) hydrogen bonds : angle 4.37295 / 3.23 ( 1596) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.385 Fit side-chains REVERT: A 213 LEU cc_start: 0.7799 (tt) cc_final: 0.7593 (tt) REVERT: A 258 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: B 164 LEU cc_start: 0.7957 (mt) cc_final: 0.7753 (mp) REVERT: B 189 LEU cc_start: 0.7076 (tt) cc_final: 0.6764 (mm) REVERT: E 263 MET cc_start: 0.2272 (ptp) cc_final: 0.0774 (tpp) REVERT: E 406 MET cc_start: 0.8248 (tmm) cc_final: 0.7701 (ttt) REVERT: E 481 ARG cc_start: 0.7401 (mtm-85) cc_final: 0.7176 (ttm170) REVERT: E 585 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7130 (pp30) REVERT: E 615 VAL cc_start: 0.8487 (t) cc_final: 0.8199 (p) REVERT: E 640 THR cc_start: 0.7862 (t) cc_final: 0.7604 (m) REVERT: E 671 MET cc_start: 0.7953 (mmt) cc_final: 0.7560 (mtp) REVERT: E 682 GLU cc_start: 0.7503 (tp30) cc_final: 0.7271 (tp30) REVERT: E 712 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7332 (mtm-85) REVERT: E 854 ARG cc_start: 0.7773 (mtp85) cc_final: 0.7504 (mtp85) REVERT: E 955 VAL cc_start: 0.8252 (OUTLIER) cc_final: 0.7995 (p) REVERT: E 996 THR cc_start: 0.7915 (m) cc_final: 0.7647 (p) REVERT: E 1039 SER cc_start: 0.3852 (OUTLIER) cc_final: 0.3504 (p) outliers start: 30 outliers final: 11 residues processed: 198 average time/residue: 0.6010 time to fit residues: 128.5348 Evaluate side-chains 192 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 468 TYR Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 778 GLU Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 955 VAL Chi-restraints excluded: chain E residue 1031 TYR Chi-restraints excluded: chain E residue 1032 LEU Chi-restraints excluded: chain E residue 1039 SER Chi-restraints excluded: chain E residue 1068 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 488 GLN ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 HIS E 979 GLN E1117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.188267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.154135 restraints weight = 16112.617| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.98 r_work: 0.3851 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 12359 Z= 0.282 Angle : 0.788 13.141 17088 Z= 0.412 Chirality : 0.050 0.247 1970 Planarity : 0.007 0.054 1966 Dihedral : 19.422 104.400 2235 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.20 % Allowed : 14.35 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.21), residues: 1380 helix: 0.40 (0.19), residues: 680 sheet: -0.93 (0.58), residues: 84 loop : -1.88 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 507 TYR 0.030 0.003 TYR A 341 PHE 0.022 0.003 PHE E 721 TRP 0.016 0.002 TRP E1070 HIS 0.014 0.002 HIS E1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.28 (12359) covalent geometry : angle 0.78782 / 0.41 (17088) hydrogen bonds : bond 0.07509 / 4.93 ( 568) hydrogen bonds : angle 4.50855 / 3.31 ( 1596) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6058 (t80) REVERT: B 189 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6766 (mm) REVERT: B 220 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8384 (tt) REVERT: B 328 MET cc_start: 0.6342 (tmm) cc_final: 0.5450 (tmm) REVERT: E 226 LEU cc_start: 0.4550 (mm) cc_final: 0.4257 (mt) REVERT: E 406 MET cc_start: 0.8344 (tmm) cc_final: 0.7739 (ttt) REVERT: E 481 ARG cc_start: 0.7422 (mtm-85) cc_final: 0.7153 (ttm170) REVERT: E 585 GLN cc_start: 0.7606 (tm-30) cc_final: 0.7176 (pp30) REVERT: E 588 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7084 (mt0) REVERT: E 640 THR cc_start: 0.7966 (t) cc_final: 0.7688 (m) REVERT: E 682 GLU cc_start: 0.7540 (tp30) cc_final: 0.7304 (tp30) REVERT: E 803 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7115 (mtm180) REVERT: E 853 LYS cc_start: 0.7775 (mtmm) cc_final: 0.7562 (mtmm) REVERT: E 996 THR cc_start: 0.8009 (m) cc_final: 0.7725 (p) REVERT: E 1040 LEU cc_start: 0.3553 (OUTLIER) cc_final: 0.2946 (mp) outliers start: 46 outliers final: 21 residues processed: 207 average time/residue: 0.6458 time to fit residues: 144.1829 Evaluate side-chains 208 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 468 TYR Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 588 GLN Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 687 CYS Chi-restraints excluded: chain E residue 778 GLU Chi-restraints excluded: chain E residue 803 ARG Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 955 VAL Chi-restraints excluded: chain E residue 1031 TYR Chi-restraints excluded: chain E residue 1040 LEU Chi-restraints excluded: chain E residue 1068 VAL Chi-restraints excluded: chain E residue 1069 GLU Chi-restraints excluded: chain E residue 1173 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 58 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 0.0370 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 128 optimal weight: 0.0980 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 ASN E 488 GLN ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 HIS E1063 HIS E1117 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.193531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.160060 restraints weight = 16129.303| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 1.95 r_work: 0.3920 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12359 Z= 0.132 Angle : 0.604 9.706 17088 Z= 0.322 Chirality : 0.041 0.216 1970 Planarity : 0.005 0.050 1966 Dihedral : 19.250 106.225 2235 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.65 % Allowed : 17.73 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.22), residues: 1380 helix: 0.98 (0.20), residues: 698 sheet: -0.72 (0.53), residues: 101 loop : -1.81 (0.23), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 507 TYR 0.018 0.001 TYR E 468 PHE 0.017 0.001 PHE E 802 TRP 0.009 0.001 TRP E 567 HIS 0.003 0.001 HIS E1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 (12359) covalent geometry : angle 0.60386 / 0.32 (17088) hydrogen bonds : bond 0.04654 / 3.05 ( 568) hydrogen bonds : angle 4.08633 / 2.98 ( 1596) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 213 LEU cc_start: 0.7843 (tt) cc_final: 0.7623 (tp) REVERT: A 258 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.5595 (t80) REVERT: B 189 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6833 (mm) REVERT: B 328 MET cc_start: 0.6320 (tmm) cc_final: 0.5426 (tmm) REVERT: E 226 LEU cc_start: 0.4035 (mm) cc_final: 0.3813 (mt) REVERT: E 481 ARG cc_start: 0.7389 (mtm-85) cc_final: 0.7141 (ttm170) REVERT: E 585 GLN cc_start: 0.7577 (tm-30) cc_final: 0.7108 (pp30) REVERT: E 640 THR cc_start: 0.7861 (t) cc_final: 0.7595 (m) REVERT: E 682 GLU cc_start: 0.7466 (tp30) cc_final: 0.7244 (tp30) REVERT: E 712 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7285 (mtm-85) REVERT: E 865 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6534 (pm20) REVERT: E 996 THR cc_start: 0.7770 (m) cc_final: 0.7482 (p) outliers start: 29 outliers final: 7 residues processed: 181 average time/residue: 0.6475 time to fit residues: 126.4982 Evaluate side-chains 179 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 468 TYR Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 865 GLU Chi-restraints excluded: chain E residue 1031 TYR Chi-restraints excluded: chain E residue 1032 LEU Chi-restraints excluded: chain E residue 1068 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 44 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 137 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 488 GLN ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 722 GLN E 920 HIS E1117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.192165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.158550 restraints weight = 16050.410| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 1.96 r_work: 0.3900 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12359 Z= 0.152 Angle : 0.622 10.004 17088 Z= 0.326 Chirality : 0.042 0.195 1970 Planarity : 0.005 0.064 1966 Dihedral : 19.118 105.281 2234 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.29 % Allowed : 18.19 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.23), residues: 1380 helix: 1.19 (0.20), residues: 687 sheet: -0.55 (0.57), residues: 95 loop : -1.79 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 507 TYR 0.020 0.002 TYR E 468 PHE 0.020 0.001 PHE E 802 TRP 0.010 0.001 TRP A 194 HIS 0.006 0.001 HIS E1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (12359) covalent geometry : angle 0.62155 / 0.33 (17088) hydrogen bonds : bond 0.04998 / 3.27 ( 568) hydrogen bonds : angle 4.00452 / 2.92 ( 1596) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 213 LEU cc_start: 0.7922 (tt) cc_final: 0.7664 (tp) REVERT: A 258 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.5597 (t80) REVERT: B 189 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6767 (mm) REVERT: B 328 MET cc_start: 0.6335 (tmm) cc_final: 0.5447 (tmm) REVERT: E 226 LEU cc_start: 0.4395 (mm) cc_final: 0.4156 (mt) REVERT: E 481 ARG cc_start: 0.7415 (mtm-85) cc_final: 0.7166 (ttm170) REVERT: E 511 ARG cc_start: 0.7754 (ttm170) cc_final: 0.6509 (ttm-80) REVERT: E 585 GLN cc_start: 0.7568 (tm-30) cc_final: 0.7122 (pp30) REVERT: E 588 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6965 (mt0) REVERT: E 640 THR cc_start: 0.7861 (t) cc_final: 0.7593 (m) REVERT: E 682 GLU cc_start: 0.7464 (tp30) cc_final: 0.7240 (tp30) REVERT: E 712 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7368 (mtm-85) REVERT: E 996 THR cc_start: 0.7876 (m) cc_final: 0.7536 (p) outliers start: 36 outliers final: 15 residues processed: 182 average time/residue: 0.6330 time to fit residues: 124.6519 Evaluate side-chains 182 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 529 HIS Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 588 GLN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 778 GLU Chi-restraints excluded: chain E residue 1031 TYR Chi-restraints excluded: chain E residue 1032 LEU Chi-restraints excluded: chain E residue 1068 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 0.0770 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 HIS E 488 GLN ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 HIS E1117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.192060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.158213 restraints weight = 16107.738| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 1.97 r_work: 0.3901 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12359 Z= 0.149 Angle : 0.611 9.898 17088 Z= 0.321 Chirality : 0.042 0.190 1970 Planarity : 0.005 0.054 1966 Dihedral : 19.042 103.915 2234 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.47 % Allowed : 18.74 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.23), residues: 1380 helix: 1.28 (0.20), residues: 688 sheet: -0.52 (0.58), residues: 95 loop : -1.77 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 375 TYR 0.025 0.002 TYR E 468 PHE 0.016 0.001 PHE E 802 TRP 0.010 0.001 TRP E 707 HIS 0.005 0.001 HIS E1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (12359) covalent geometry : angle 0.61057 / 0.32 (17088) hydrogen bonds : bond 0.04789 / 3.14 ( 568) hydrogen bonds : angle 3.95470 / 2.86 ( 1596) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 0.415 Fit side-chains REVERT: A 213 LEU cc_start: 0.7954 (tt) cc_final: 0.7694 (tp) REVERT: A 258 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.5646 (t80) REVERT: A 339 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: B 189 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6756 (mm) REVERT: B 328 MET cc_start: 0.6369 (tmm) cc_final: 0.5477 (tmm) REVERT: E 226 LEU cc_start: 0.4504 (mm) cc_final: 0.4274 (mt) REVERT: E 481 ARG cc_start: 0.7419 (mtm-85) cc_final: 0.7186 (ttm170) REVERT: E 511 ARG cc_start: 0.7746 (ttm170) cc_final: 0.6481 (ttm-80) REVERT: E 585 GLN cc_start: 0.7531 (tm-30) cc_final: 0.7076 (pp30) REVERT: E 588 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6972 (mt0) REVERT: E 640 THR cc_start: 0.7853 (t) cc_final: 0.7590 (m) REVERT: E 682 GLU cc_start: 0.7457 (tp30) cc_final: 0.7234 (tp30) REVERT: E 712 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7332 (mtm-85) REVERT: E 865 GLU cc_start: 0.6788 (pm20) cc_final: 0.6542 (pm20) REVERT: E 996 THR cc_start: 0.7834 (m) cc_final: 0.7456 (p) outliers start: 38 outliers final: 18 residues processed: 184 average time/residue: 0.5945 time to fit residues: 118.7448 Evaluate side-chains 185 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 588 GLN Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 989 VAL Chi-restraints excluded: chain E residue 1031 TYR Chi-restraints excluded: chain E residue 1032 LEU Chi-restraints excluded: chain E residue 1068 VAL Chi-restraints excluded: chain E residue 1069 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 114 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 140 optimal weight: 10.0000 chunk 44 optimal weight: 0.3980 chunk 127 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 488 GLN ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 HIS E1117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.192564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.158770 restraints weight = 16117.787| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 1.97 r_work: 0.3907 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12359 Z= 0.134 Angle : 0.597 10.723 17088 Z= 0.313 Chirality : 0.041 0.197 1970 Planarity : 0.005 0.046 1966 Dihedral : 18.941 102.301 2234 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.83 % Allowed : 19.84 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.23), residues: 1380 helix: 1.42 (0.20), residues: 688 sheet: -0.43 (0.56), residues: 100 loop : -1.78 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 375 TYR 0.011 0.001 TYR E1004 PHE 0.015 0.001 PHE E 802 TRP 0.012 0.001 TRP B 200 HIS 0.004 0.001 HIS E1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (12359) covalent geometry : angle 0.59702 / 0.31 (17088) hydrogen bonds : bond 0.04453 / 2.92 ( 568) hydrogen bonds : angle 3.87947 / 2.79 ( 1596) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.347 Fit side-chains REVERT: A 258 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.5545 (t80) REVERT: B 189 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6741 (mm) REVERT: B 328 MET cc_start: 0.6360 (tmm) cc_final: 0.5458 (tmm) REVERT: E 226 LEU cc_start: 0.4628 (mm) cc_final: 0.4417 (mt) REVERT: E 406 MET cc_start: 0.8224 (tmm) cc_final: 0.7560 (ttt) REVERT: E 481 ARG cc_start: 0.7438 (mtm-85) cc_final: 0.7208 (ttm170) REVERT: E 488 GLN cc_start: 0.7782 (tt0) cc_final: 0.7513 (tt0) REVERT: E 511 ARG cc_start: 0.7749 (ttm170) cc_final: 0.6503 (ttm-80) REVERT: E 585 GLN cc_start: 0.7520 (tm-30) cc_final: 0.7080 (pp30) REVERT: E 588 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6921 (mt0) REVERT: E 640 THR cc_start: 0.7821 (t) cc_final: 0.7572 (m) REVERT: E 682 GLU cc_start: 0.7440 (tp30) cc_final: 0.7221 (tp30) REVERT: E 712 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7318 (mtm-85) REVERT: E 781 TYR cc_start: 0.7639 (m-80) cc_final: 0.7272 (m-80) REVERT: E 996 THR cc_start: 0.7887 (m) cc_final: 0.7512 (p) outliers start: 31 outliers final: 15 residues processed: 182 average time/residue: 0.6121 time to fit residues: 120.6428 Evaluate side-chains 185 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 529 HIS Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 588 GLN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 1023 GLU Chi-restraints excluded: chain E residue 1031 TYR Chi-restraints excluded: chain E residue 1032 LEU Chi-restraints excluded: chain E residue 1068 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 139 optimal weight: 30.0000 chunk 137 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 81 optimal weight: 0.0570 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.191594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.157642 restraints weight = 15931.976| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.96 r_work: 0.3895 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12359 Z= 0.151 Angle : 0.613 10.424 17088 Z= 0.321 Chirality : 0.041 0.184 1970 Planarity : 0.005 0.047 1966 Dihedral : 18.856 101.196 2234 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.11 % Allowed : 19.74 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.23), residues: 1380 helix: 1.43 (0.20), residues: 689 sheet: -0.43 (0.56), residues: 100 loop : -1.81 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 507 TYR 0.013 0.002 TYR A 258 PHE 0.014 0.001 PHE E 802 TRP 0.010 0.001 TRP E 707 HIS 0.005 0.001 HIS E1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (12359) covalent geometry : angle 0.61305 / 0.32 (17088) hydrogen bonds : bond 0.04726 / 3.10 ( 568) hydrogen bonds : angle 3.90580 / 2.82 ( 1596) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.423 Fit side-chains REVERT: A 213 LEU cc_start: 0.7937 (tt) cc_final: 0.7686 (tp) REVERT: A 258 TYR cc_start: 0.7203 (OUTLIER) cc_final: 0.5642 (t80) REVERT: B 164 LEU cc_start: 0.7943 (mp) cc_final: 0.7667 (mp) REVERT: B 189 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6743 (mm) REVERT: B 328 MET cc_start: 0.6361 (tmm) cc_final: 0.5436 (tmm) REVERT: E 406 MET cc_start: 0.8231 (tmm) cc_final: 0.7516 (ttt) REVERT: E 481 ARG cc_start: 0.7441 (mtm-85) cc_final: 0.7137 (ttm-80) REVERT: E 488 GLN cc_start: 0.7783 (tt0) cc_final: 0.7526 (tt0) REVERT: E 511 ARG cc_start: 0.7734 (ttm170) cc_final: 0.6485 (ttm-80) REVERT: E 585 GLN cc_start: 0.7532 (tm-30) cc_final: 0.7072 (pp30) REVERT: E 588 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6942 (mt0) REVERT: E 640 THR cc_start: 0.7841 (t) cc_final: 0.7597 (m) REVERT: E 682 GLU cc_start: 0.7435 (tp30) cc_final: 0.7209 (tp30) REVERT: E 712 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7310 (mtm-85) REVERT: E 996 THR cc_start: 0.7886 (m) cc_final: 0.7511 (p) outliers start: 34 outliers final: 19 residues processed: 177 average time/residue: 0.6157 time to fit residues: 118.2014 Evaluate side-chains 187 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 588 GLN Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 778 GLU Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 1023 GLU Chi-restraints excluded: chain E residue 1031 TYR Chi-restraints excluded: chain E residue 1032 LEU Chi-restraints excluded: chain E residue 1068 VAL Chi-restraints excluded: chain E residue 1069 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 82 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.0010 chunk 104 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 15 optimal weight: 0.0060 chunk 137 optimal weight: 0.8980 overall best weight: 0.3720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.193366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.159699 restraints weight = 16087.559| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 1.97 r_work: 0.3923 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3774 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12359 Z= 0.120 Angle : 0.584 11.063 17088 Z= 0.304 Chirality : 0.040 0.180 1970 Planarity : 0.005 0.045 1966 Dihedral : 18.758 100.264 2234 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.29 % Allowed : 20.48 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.23), residues: 1380 helix: 1.56 (0.21), residues: 691 sheet: -0.41 (0.57), residues: 101 loop : -1.69 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 507 TYR 0.010 0.001 TYR E1004 PHE 0.015 0.001 PHE E 802 TRP 0.009 0.001 TRP E 707 HIS 0.008 0.001 HIS E 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (12359) covalent geometry : angle 0.58362 / 0.30 (17088) hydrogen bonds : bond 0.04031 / 2.64 ( 568) hydrogen bonds : angle 3.81484 / 2.74 ( 1596) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.414 Fit side-chains REVERT: A 213 LEU cc_start: 0.7863 (tt) cc_final: 0.7620 (tp) REVERT: A 258 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.5471 (t80) REVERT: A 339 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: B 203 MET cc_start: 0.8045 (mmm) cc_final: 0.7807 (mmm) REVERT: B 328 MET cc_start: 0.6372 (tmm) cc_final: 0.5467 (tmm) REVERT: E 406 MET cc_start: 0.8214 (tmm) cc_final: 0.7497 (ttt) REVERT: E 481 ARG cc_start: 0.7443 (mtm-85) cc_final: 0.7131 (ttm-80) REVERT: E 488 GLN cc_start: 0.7801 (tt0) cc_final: 0.7543 (tt0) REVERT: E 511 ARG cc_start: 0.7731 (ttm170) cc_final: 0.6473 (ttm-80) REVERT: E 585 GLN cc_start: 0.7467 (tm-30) cc_final: 0.7031 (pp30) REVERT: E 588 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6914 (mt0) REVERT: E 640 THR cc_start: 0.7798 (t) cc_final: 0.7554 (m) REVERT: E 682 GLU cc_start: 0.7429 (tp30) cc_final: 0.7203 (tp30) REVERT: E 712 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7162 (mtm-85) REVERT: E 996 THR cc_start: 0.7779 (m) cc_final: 0.7394 (p) outliers start: 25 outliers final: 15 residues processed: 174 average time/residue: 0.6365 time to fit residues: 119.9055 Evaluate side-chains 179 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 529 HIS Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 588 GLN Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 1023 GLU Chi-restraints excluded: chain E residue 1031 TYR Chi-restraints excluded: chain E residue 1032 LEU Chi-restraints excluded: chain E residue 1069 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 11 optimal weight: 0.0070 chunk 108 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.0270 chunk 140 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 847 ASN E1117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.190043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.156799 restraints weight = 15995.802| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.87 r_work: 0.3886 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12359 Z= 0.179 Angle : 0.658 10.714 17088 Z= 0.340 Chirality : 0.043 0.183 1970 Planarity : 0.005 0.049 1966 Dihedral : 18.720 100.042 2234 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.01 % Allowed : 20.75 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.23), residues: 1380 helix: 1.38 (0.20), residues: 696 sheet: -0.47 (0.58), residues: 96 loop : -1.80 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 507 TYR 0.018 0.002 TYR A 258 PHE 0.020 0.002 PHE A 228 TRP 0.011 0.002 TRP E 707 HIS 0.006 0.001 HIS E1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (12359) covalent geometry : angle 0.65837 / 0.34 (17088) hydrogen bonds : bond 0.05253 / 3.44 ( 568) hydrogen bonds : angle 3.97720 / 2.88 ( 1596) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.429 Fit side-chains REVERT: A 213 LEU cc_start: 0.7936 (tt) cc_final: 0.7681 (tp) REVERT: A 258 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.5737 (t80) REVERT: A 339 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: B 328 MET cc_start: 0.6374 (tmm) cc_final: 0.5450 (tmm) REVERT: E 406 MET cc_start: 0.8293 (tmm) cc_final: 0.7570 (ttt) REVERT: E 481 ARG cc_start: 0.7458 (mtm-85) cc_final: 0.7165 (ttm-80) REVERT: E 488 GLN cc_start: 0.7859 (tt0) cc_final: 0.7568 (tt0) REVERT: E 511 ARG cc_start: 0.7734 (ttm170) cc_final: 0.6516 (ttm-80) REVERT: E 585 GLN cc_start: 0.7417 (tm-30) cc_final: 0.7032 (pp30) REVERT: E 588 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6904 (mt0) REVERT: E 640 THR cc_start: 0.7874 (t) cc_final: 0.7641 (m) REVERT: E 682 GLU cc_start: 0.7466 (tp30) cc_final: 0.7238 (tp30) REVERT: E 712 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7372 (mtm-85) REVERT: E 781 TYR cc_start: 0.7671 (m-80) cc_final: 0.7273 (m-80) REVERT: E 996 THR cc_start: 0.7848 (m) cc_final: 0.7520 (p) outliers start: 22 outliers final: 15 residues processed: 171 average time/residue: 0.6283 time to fit residues: 116.2260 Evaluate side-chains 175 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 588 GLN Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 778 GLU Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 1023 GLU Chi-restraints excluded: chain E residue 1031 TYR Chi-restraints excluded: chain E residue 1032 LEU Chi-restraints excluded: chain E residue 1069 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 94 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 51 optimal weight: 0.0670 chunk 63 optimal weight: 0.7980 chunk 71 optimal weight: 0.0670 chunk 19 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.192435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.159392 restraints weight = 16052.176| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.91 r_work: 0.3918 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12359 Z= 0.124 Angle : 0.600 10.745 17088 Z= 0.309 Chirality : 0.040 0.178 1970 Planarity : 0.005 0.045 1966 Dihedral : 18.662 99.848 2234 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.55 % Allowed : 21.48 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.23), residues: 1380 helix: 1.52 (0.21), residues: 697 sheet: -0.40 (0.57), residues: 101 loop : -1.74 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 507 TYR 0.011 0.001 TYR E1004 PHE 0.014 0.001 PHE E 802 TRP 0.010 0.001 TRP E 707 HIS 0.004 0.001 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (12359) covalent geometry : angle 0.59991 / 0.31 (17088) hydrogen bonds : bond 0.04184 / 2.74 ( 568) hydrogen bonds : angle 3.84925 / 2.77 ( 1596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5389.66 seconds wall clock time: 92 minutes 20.73 seconds (5540.73 seconds total)