Starting phenix.real_space_refine on Sat Aug 23 12:19:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8v_42028/08_2025/8u8v_42028.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8v_42028/08_2025/8u8v_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8u8v_42028/08_2025/8u8v_42028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8v_42028/08_2025/8u8v_42028.map" model { file = "/net/cci-nas-00/data/ceres_data/8u8v_42028/08_2025/8u8v_42028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8v_42028/08_2025/8u8v_42028.cif" } 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-2.0-5787/lib/python3.9/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: 3.11, per 1000 atoms: 0.26 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: 0.84 Conformation dependent library (CDL) restraints added in 487.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.48 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: 2.38 Time building geometry restraints manager: 1.16 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=" 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=" N ASP E 954 " pdb=" CA ASP E 954 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.22e-02 6.72e+03 1.13e+01 bond pdb=" N ILE E1050 " pdb=" CA ILE E1050 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.21e-02 6.83e+03 1.06e+01 ... (remaining 12354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 16540 2.27 - 4.54: 438 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 - 0.127: 1905 0.127 - 0.253: 48 0.253 - 0.380: 0 0.380 - 0.506: 5 0.506 - 0.633: 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 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.00e+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 2.35 -2.97 -0.63 2.00e-01 2.50e+01 9.83e+00 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 2.35 -2.88 -0.53 2.00e-01 2.50e+01 7.09e+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: 1.830 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.860 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5075 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= 0.299 Angle : 0.891 11.358 17088 Z= 0.525 Chirality : 0.069 0.633 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 aren 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 covalent geometry : bond 0.00507 (12359) covalent geometry : angle 0.89069 (17088) hydrogen bonds : bond 0.19721 ( 568) hydrogen bonds : angle 6.48521 ( 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 : 0.397 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: 0.7286 (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: 0.5918 (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: 0.5845 time to fit residues: 139.9798 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 : 0.261 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 302 GLN A 346 GLN ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 HIS E 893 GLN E 903 ASN E 945 ASN E 979 GLN E1051 GLN E1063 HIS ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1117 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.196205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.164123 restraints weight = 16172.674| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.06 r_work: 0.3949 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12359 Z= 0.148 Angle : 0.613 9.719 17088 Z= 0.322 Chirality : 0.040 0.196 1970 Planarity : 0.005 0.055 1966 Dihedral : 19.466 103.357 2235 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.65 % Allowed : 11.24 % Favored : 86.11 % 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 aren not related in a simple way. whole: -0.56 (0.22), residues: 1380 helix: 0.76 (0.20), residues: 699 sheet: -0.67 (0.53), residues: 98 loop : -1.73 (0.23), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1048 TYR 0.020 0.002 TYR E 468 PHE 0.015 0.001 PHE E 802 TRP 0.010 0.001 TRP E 707 HIS 0.004 0.001 HIS E 916 Details of bonding type rmsd covalent geometry : bond 0.00321 (12359) covalent geometry : angle 0.61342 (17088) hydrogen bonds : bond 0.04995 ( 568) hydrogen bonds : angle 4.18639 ( 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 212 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.251 Fit side-chains REVERT: A 213 LEU cc_start: 0.7826 (tt) cc_final: 0.7619 (tt) REVERT: A 258 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.6757 (m-80) REVERT: B 164 LEU cc_start: 0.7929 (mt) cc_final: 0.7709 (mp) REVERT: B 189 LEU cc_start: 0.7062 (tt) cc_final: 0.6737 (mm) REVERT: E 263 MET cc_start: 0.2261 (ptp) cc_final: 0.0750 (tpp) REVERT: E 406 MET cc_start: 0.8222 (tmm) cc_final: 0.7638 (ttt) REVERT: E 481 ARG cc_start: 0.7418 (mtm-85) cc_final: 0.7173 (ttm170) REVERT: E 585 GLN cc_start: 0.7572 (tm-30) cc_final: 0.7063 (pp30) REVERT: E 615 VAL cc_start: 0.8452 (t) cc_final: 0.8157 (p) REVERT: E 640 THR cc_start: 0.7864 (t) cc_final: 0.7602 (m) REVERT: E 671 MET cc_start: 0.7994 (mmt) cc_final: 0.7605 (mtp) REVERT: E 682 GLU cc_start: 0.7499 (tp30) cc_final: 0.7259 (tp30) REVERT: E 854 ARG cc_start: 0.7790 (mtp85) cc_final: 0.7541 (mtp85) REVERT: E 955 VAL cc_start: 0.8199 (m) cc_final: 0.7969 (p) REVERT: E 996 THR cc_start: 0.7869 (m) cc_final: 0.7548 (p) REVERT: E 1039 SER cc_start: 0.3759 (OUTLIER) cc_final: 0.3267 (p) outliers start: 29 outliers final: 13 residues processed: 193 average time/residue: 0.6077 time to fit residues: 126.0042 Evaluate side-chains 191 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 253 MET 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 778 GLU 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 Chi-restraints excluded: chain E residue 1139 CYS 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: 3.9990 chunk 78 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 836 HIS 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 = 0.4335 r_free = 0.4335 target = 0.186586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.152694 restraints weight = 16022.934| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.16 r_work: 0.3820 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 12359 Z= 0.311 Angle : 0.805 12.294 17088 Z= 0.414 Chirality : 0.048 0.197 1970 Planarity : 0.007 0.055 1966 Dihedral : 19.417 103.672 2234 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.20 % Allowed : 14.08 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.21), residues: 1380 helix: 0.35 (0.19), residues: 691 sheet: -0.94 (0.58), residues: 84 loop : -1.94 (0.22), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 375 TYR 0.034 0.004 TYR E 468 PHE 0.024 0.003 PHE E1119 TRP 0.016 0.003 TRP E1070 HIS 0.014 0.002 HIS E1131 Details of bonding type rmsd covalent geometry : bond 0.00738 (12359) covalent geometry : angle 0.80506 (17088) hydrogen bonds : bond 0.07667 ( 568) hydrogen bonds : angle 4.53668 ( 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 : 0.285 Fit side-chains revert: symmetry clash REVERT: A 258 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6102 (t80) REVERT: B 164 LEU cc_start: 0.8017 (mt) cc_final: 0.7805 (mp) REVERT: B 189 LEU cc_start: 0.7357 (tt) cc_final: 0.6834 (mm) REVERT: B 220 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8365 (tt) REVERT: B 328 MET cc_start: 0.6351 (tmm) cc_final: 0.5448 (tmm) REVERT: E 226 LEU cc_start: 0.4949 (mm) cc_final: 0.4727 (mt) REVERT: E 372 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8405 (mmmt) REVERT: E 481 ARG cc_start: 0.7424 (mtm-85) cc_final: 0.7173 (ttm170) REVERT: E 511 ARG cc_start: 0.7773 (ttm170) cc_final: 0.6512 (ttm-80) REVERT: E 585 GLN cc_start: 0.7627 (tm-30) cc_final: 0.7138 (pp30) REVERT: E 640 THR cc_start: 0.7999 (t) cc_final: 0.7702 (m) REVERT: E 682 GLU cc_start: 0.7565 (tp30) cc_final: 0.7343 (tp30) REVERT: E 803 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7197 (mtm180) REVERT: E 922 ASP cc_start: 0.7411 (t70) cc_final: 0.7210 (t70) REVERT: E 996 THR cc_start: 0.7995 (m) cc_final: 0.7681 (p) REVERT: E 1040 LEU cc_start: 0.3583 (OUTLIER) cc_final: 0.3222 (mp) outliers start: 46 outliers final: 20 residues processed: 208 average time/residue: 0.5976 time to fit residues: 133.8794 Evaluate side-chains 203 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE 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 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 473 LEU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 660 SER 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 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: 0.0470 chunk 69 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 488 GLN ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 617 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 = 0.4375 r_free = 0.4375 target = 0.190836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.157775 restraints weight = 16054.265| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.87 r_work: 0.3899 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12359 Z= 0.155 Angle : 0.616 10.891 17088 Z= 0.323 Chirality : 0.040 0.160 1970 Planarity : 0.005 0.049 1966 Dihedral : 19.214 105.907 2234 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.29 % Allowed : 17.55 % Favored : 79.16 % 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 aren not related in a simple way. whole: -0.56 (0.22), residues: 1380 helix: 0.88 (0.20), residues: 689 sheet: -0.64 (0.56), residues: 96 loop : -1.86 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 507 TYR 0.028 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 covalent geometry : bond 0.00340 (12359) covalent geometry : angle 0.61604 (17088) hydrogen bonds : bond 0.05024 ( 568) hydrogen bonds : angle 4.13339 ( 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 215 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 213 LEU cc_start: 0.7934 (tt) cc_final: 0.7688 (tp) REVERT: A 258 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.5710 (t80) REVERT: B 189 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6851 (mm) REVERT: B 220 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8352 (tt) REVERT: B 328 MET cc_start: 0.6297 (tmm) cc_final: 0.5369 (tmm) REVERT: E 372 LYS cc_start: 0.8480 (mmmt) cc_final: 0.7672 (mmmt) REVERT: E 375 ARG cc_start: 0.7897 (ttm-80) cc_final: 0.7453 (ttm110) REVERT: E 406 MET cc_start: 0.8338 (tmm) cc_final: 0.7608 (ttt) REVERT: E 481 ARG cc_start: 0.7338 (mtm-85) cc_final: 0.7106 (ttm170) REVERT: E 511 ARG cc_start: 0.7681 (ttm170) cc_final: 0.6395 (ttm-80) REVERT: E 585 GLN cc_start: 0.7515 (tm-30) cc_final: 0.7071 (pp30) REVERT: E 640 THR cc_start: 0.7875 (t) cc_final: 0.7609 (m) REVERT: E 682 GLU cc_start: 0.7415 (tp30) cc_final: 0.7195 (tp30) REVERT: E 712 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7270 (mtm-85) REVERT: E 996 THR cc_start: 0.7799 (m) cc_final: 0.7546 (p) outliers start: 36 outliers final: 13 residues processed: 197 average time/residue: 0.5780 time to fit residues: 122.2968 Evaluate side-chains 192 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 258 TYR 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 273 VAL 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 638 THR Chi-restraints excluded: chain E residue 712 ARG 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 44 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 137 optimal weight: 0.0370 chunk 99 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 24 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4382 r_free = 0.4382 target = 0.191348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.157817 restraints weight = 15992.396| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.94 r_work: 0.3893 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2872 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= 0.141 Angle : 0.588 9.984 17088 Z= 0.306 Chirality : 0.039 0.168 1970 Planarity : 0.005 0.052 1966 Dihedral : 19.045 104.901 2234 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.20 % Allowed : 17.82 % Favored : 77.97 % 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 aren not related in a simple way. whole: -0.23 (0.23), residues: 1380 helix: 1.21 (0.20), residues: 692 sheet: -0.57 (0.55), residues: 101 loop : -1.80 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 507 TYR 0.024 0.002 TYR E 468 PHE 0.018 0.001 PHE E 802 TRP 0.010 0.001 TRP E 707 HIS 0.005 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00310 (12359) covalent geometry : angle 0.58788 (17088) hydrogen bonds : bond 0.04624 ( 568) hydrogen bonds : angle 3.92518 ( 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 229 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 258 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.5640 (t80) REVERT: B 164 LEU cc_start: 0.8035 (mt) cc_final: 0.7783 (mp) REVERT: B 189 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6837 (mm) REVERT: B 328 MET cc_start: 0.6305 (tmm) cc_final: 0.5389 (tmm) REVERT: E 372 LYS cc_start: 0.8483 (mmmt) cc_final: 0.7734 (mmmt) REVERT: E 375 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7455 (ttm110) REVERT: E 406 MET cc_start: 0.8308 (tmm) cc_final: 0.7590 (ttt) REVERT: E 481 ARG cc_start: 0.7377 (mtm-85) cc_final: 0.7083 (ttm-80) REVERT: E 511 ARG cc_start: 0.7751 (ttm170) cc_final: 0.6483 (ttm-80) REVERT: E 585 GLN cc_start: 0.7511 (tm-30) cc_final: 0.7054 (pp30) REVERT: E 588 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6952 (mt0) REVERT: E 640 THR cc_start: 0.7820 (t) cc_final: 0.7551 (m) REVERT: E 682 GLU cc_start: 0.7412 (tp30) cc_final: 0.7186 (tp30) REVERT: E 712 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7235 (mtm-85) REVERT: E 781 TYR cc_start: 0.7661 (m-80) cc_final: 0.7291 (m-80) REVERT: E 866 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7015 (mm-30) REVERT: E 996 THR cc_start: 0.7833 (m) cc_final: 0.7487 (p) outliers start: 46 outliers final: 22 residues processed: 206 average time/residue: 0.5317 time to fit residues: 118.7642 Evaluate side-chains 203 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 189 LEU 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 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 638 THR Chi-restraints excluded: chain E residue 687 CYS Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 866 GLU Chi-restraints excluded: chain E residue 939 VAL Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 989 VAL 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 1173 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4370 r_free = 0.4370 target = 0.189717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.156156 restraints weight = 16032.169| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.95 r_work: 0.3895 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12359 Z= 0.146 Angle : 0.594 10.766 17088 Z= 0.307 Chirality : 0.039 0.163 1970 Planarity : 0.005 0.047 1966 Dihedral : 18.899 103.447 2234 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.84 % Allowed : 17.46 % Favored : 77.70 % 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 aren not related in a simple way. whole: -0.14 (0.23), residues: 1380 helix: 1.34 (0.20), residues: 691 sheet: -0.47 (0.58), residues: 96 loop : -1.83 (0.23), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 507 TYR 0.021 0.002 TYR E 468 PHE 0.015 0.001 PHE E 802 TRP 0.011 0.001 TRP E 707 HIS 0.005 0.001 HIS E1131 Details of bonding type rmsd covalent geometry : bond 0.00325 (12359) covalent geometry : angle 0.59438 (17088) hydrogen bonds : bond 0.04653 ( 568) hydrogen bonds : angle 3.86654 ( 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 228 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 0.330 Fit side-chains REVERT: A 213 LEU cc_start: 0.7928 (tt) cc_final: 0.7670 (tp) REVERT: A 258 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.5655 (t80) REVERT: B 164 LEU cc_start: 0.7991 (mt) cc_final: 0.7730 (mp) REVERT: B 328 MET cc_start: 0.6400 (tmm) cc_final: 0.5485 (tmm) REVERT: E 372 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8281 (mmmt) REVERT: E 406 MET cc_start: 0.8273 (tmm) cc_final: 0.7613 (ttt) REVERT: E 481 ARG cc_start: 0.7420 (mtm-85) cc_final: 0.7121 (ttm-80) REVERT: E 488 GLN cc_start: 0.7918 (tt0) cc_final: 0.7645 (tt0) REVERT: E 511 ARG cc_start: 0.7744 (ttm170) cc_final: 0.6482 (ttm-80) REVERT: E 585 GLN cc_start: 0.7436 (tm-30) cc_final: 0.7007 (pp30) REVERT: E 588 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6917 (mt0) REVERT: E 640 THR cc_start: 0.7877 (t) cc_final: 0.7642 (m) REVERT: E 682 GLU cc_start: 0.7448 (tp30) cc_final: 0.7223 (tp30) REVERT: E 712 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7237 (mtm-85) REVERT: E 781 TYR cc_start: 0.7663 (m-80) cc_final: 0.7256 (m-80) REVERT: E 866 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7031 (mm-30) REVERT: E 996 THR cc_start: 0.7820 (m) cc_final: 0.7457 (p) outliers start: 53 outliers final: 24 residues processed: 201 average time/residue: 0.5354 time to fit residues: 116.1987 Evaluate side-chains 199 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 273 VAL 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 638 THR Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 687 CYS Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 866 GLU Chi-restraints excluded: chain E residue 939 VAL Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 1008 LEU 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 Chi-restraints excluded: chain E residue 1173 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.0170 chunk 111 optimal weight: 0.8980 chunk 114 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.191529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.158491 restraints weight = 16083.955| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 1.91 r_work: 0.3909 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12359 Z= 0.131 Angle : 0.581 9.992 17088 Z= 0.300 Chirality : 0.039 0.196 1970 Planarity : 0.005 0.046 1966 Dihedral : 18.736 101.894 2234 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.20 % Allowed : 18.37 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.23), residues: 1380 helix: 1.44 (0.20), residues: 692 sheet: -0.46 (0.56), residues: 101 loop : -1.77 (0.24), residues: 587 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 0.015 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 covalent geometry : bond 0.00282 (12359) covalent geometry : angle 0.58139 (17088) hydrogen bonds : bond 0.04272 ( 568) hydrogen bonds : angle 3.78844 ( 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 216 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.399 Fit side-chains REVERT: A 213 LEU cc_start: 0.7918 (tt) cc_final: 0.7663 (tp) REVERT: A 258 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.5586 (t80) REVERT: B 220 ILE cc_start: 0.8682 (mt) cc_final: 0.8330 (tt) REVERT: B 328 MET cc_start: 0.6392 (tmm) cc_final: 0.5479 (tmm) REVERT: E 372 LYS cc_start: 0.8453 (mmmt) cc_final: 0.8243 (mmmt) REVERT: E 406 MET cc_start: 0.8239 (tmm) cc_final: 0.7631 (ttt) REVERT: E 481 ARG cc_start: 0.7399 (mtm-85) cc_final: 0.7091 (ttm-80) REVERT: E 488 GLN cc_start: 0.7939 (tt0) cc_final: 0.7686 (tt0) REVERT: E 511 ARG cc_start: 0.7730 (ttm170) cc_final: 0.6481 (ttm-80) REVERT: E 585 GLN cc_start: 0.7375 (tm-30) cc_final: 0.6943 (pp30) REVERT: E 640 THR cc_start: 0.7841 (t) cc_final: 0.7602 (m) REVERT: E 682 GLU cc_start: 0.7428 (tp30) cc_final: 0.7210 (tp30) REVERT: E 712 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7098 (mtm-85) REVERT: E 781 TYR cc_start: 0.7661 (m-80) cc_final: 0.7251 (m-80) REVERT: E 996 THR cc_start: 0.7841 (m) cc_final: 0.7479 (p) outliers start: 46 outliers final: 24 residues processed: 195 average time/residue: 0.5453 time to fit residues: 115.1754 Evaluate side-chains 193 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 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 660 SER Chi-restraints excluded: chain E residue 687 CYS Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 1008 LEU 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 Chi-restraints excluded: chain E residue 1173 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 139 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.189200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.155871 restraints weight = 15850.623| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 1.90 r_work: 0.3875 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12359 Z= 0.170 Angle : 0.627 11.240 17088 Z= 0.322 Chirality : 0.040 0.183 1970 Planarity : 0.005 0.049 1966 Dihedral : 18.650 101.166 2234 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.30 % Allowed : 18.46 % 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 aren not related in a simple way. whole: -0.17 (0.23), residues: 1380 helix: 1.33 (0.20), residues: 696 sheet: -0.63 (0.62), residues: 86 loop : -1.85 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 507 TYR 0.021 0.002 TYR E 468 PHE 0.013 0.001 PHE E 802 TRP 0.011 0.001 TRP E 707 HIS 0.007 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00388 (12359) covalent geometry : angle 0.62688 (17088) hydrogen bonds : bond 0.05068 ( 568) hydrogen bonds : angle 3.91801 ( 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 218 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.371 Fit side-chains REVERT: A 258 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.5761 (t80) REVERT: B 220 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8338 (tt) REVERT: B 328 MET cc_start: 0.6370 (tmm) cc_final: 0.5465 (tmm) REVERT: E 406 MET cc_start: 0.8275 (tmm) cc_final: 0.7616 (ttt) REVERT: E 481 ARG cc_start: 0.7424 (mtm-85) cc_final: 0.7136 (ttm-80) REVERT: E 511 ARG cc_start: 0.7738 (ttm170) cc_final: 0.6495 (ttm-80) REVERT: E 585 GLN cc_start: 0.7368 (tm-30) cc_final: 0.6960 (pp30) REVERT: E 640 THR cc_start: 0.7871 (t) cc_final: 0.7629 (m) REVERT: E 682 GLU cc_start: 0.7428 (tp30) cc_final: 0.7214 (tp30) REVERT: E 712 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7286 (mtm-85) REVERT: E 781 TYR cc_start: 0.7689 (m-80) cc_final: 0.7261 (m-80) REVERT: E 996 THR cc_start: 0.7877 (m) cc_final: 0.7551 (p) outliers start: 47 outliers final: 31 residues processed: 191 average time/residue: 0.5292 time to fit residues: 109.2668 Evaluate side-chains 205 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 VAL 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 660 SER Chi-restraints excluded: chain E residue 687 CYS Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 778 GLU Chi-restraints excluded: chain E residue 939 VAL Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 995 MET Chi-restraints excluded: chain E residue 1008 LEU 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 Chi-restraints excluded: chain E residue 1173 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 82 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 488 GLN E 512 HIS E 847 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.190803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.157711 restraints weight = 16028.566| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.91 r_work: 0.3896 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3436 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= 0.135 Angle : 0.595 10.777 17088 Z= 0.305 Chirality : 0.039 0.170 1970 Planarity : 0.005 0.047 1966 Dihedral : 18.539 100.512 2234 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.47 % Allowed : 19.84 % Favored : 76.69 % 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 aren not related in a simple way. whole: -0.01 (0.23), residues: 1380 helix: 1.41 (0.20), residues: 700 sheet: -0.52 (0.56), residues: 101 loop : -1.76 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 507 TYR 0.012 0.001 TYR E1004 PHE 0.014 0.001 PHE E 802 TRP 0.011 0.001 TRP E 707 HIS 0.007 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00295 (12359) covalent geometry : angle 0.59494 (17088) hydrogen bonds : bond 0.04333 ( 568) hydrogen bonds : angle 3.82701 ( 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 209 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.327 Fit side-chains REVERT: A 213 LEU cc_start: 0.7963 (tt) cc_final: 0.7745 (tt) REVERT: A 258 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.5586 (t80) REVERT: B 220 ILE cc_start: 0.8724 (mt) cc_final: 0.8322 (tt) REVERT: B 328 MET cc_start: 0.6361 (tmm) cc_final: 0.5446 (tmm) REVERT: E 406 MET cc_start: 0.8254 (tmm) cc_final: 0.7577 (ttt) REVERT: E 481 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.7134 (ttm-80) REVERT: E 488 GLN cc_start: 0.7944 (tt0) cc_final: 0.7657 (tt0) REVERT: E 511 ARG cc_start: 0.7779 (ttm170) cc_final: 0.6510 (ttm-80) REVERT: E 585 GLN cc_start: 0.7308 (tm-30) cc_final: 0.6913 (pp30) REVERT: E 640 THR cc_start: 0.7849 (t) cc_final: 0.7605 (m) REVERT: E 682 GLU cc_start: 0.7456 (tp30) cc_final: 0.7243 (tp30) REVERT: E 712 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7196 (mtm-85) REVERT: E 781 TYR cc_start: 0.7672 (m-80) cc_final: 0.7257 (m-80) REVERT: E 996 THR cc_start: 0.7774 (m) cc_final: 0.7444 (p) outliers start: 38 outliers final: 26 residues processed: 191 average time/residue: 0.5029 time to fit residues: 103.8644 Evaluate side-chains 200 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 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 660 SER Chi-restraints excluded: chain E residue 687 CYS Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 939 VAL Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 1008 LEU 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 Chi-restraints excluded: chain E residue 1173 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 11 optimal weight: 0.0020 chunk 108 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 0.0670 chunk 48 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 847 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.190831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.157666 restraints weight = 16019.971| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.92 r_work: 0.3895 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12359 Z= 0.135 Angle : 0.596 10.538 17088 Z= 0.306 Chirality : 0.039 0.155 1970 Planarity : 0.005 0.046 1966 Dihedral : 18.458 99.383 2234 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.02 % Allowed : 20.29 % Favored : 76.69 % 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 aren not related in a simple way. whole: 0.03 (0.23), residues: 1380 helix: 1.45 (0.20), residues: 700 sheet: -0.55 (0.56), residues: 103 loop : -1.73 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 507 TYR 0.012 0.001 TYR E1004 PHE 0.014 0.001 PHE E 802 TRP 0.011 0.001 TRP E 707 HIS 0.008 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00295 (12359) covalent geometry : angle 0.59649 (17088) hydrogen bonds : bond 0.04330 ( 568) hydrogen bonds : angle 3.80097 ( 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 205 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.389 Fit side-chains REVERT: A 213 LEU cc_start: 0.7957 (tt) cc_final: 0.7748 (tt) REVERT: A 258 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.5567 (t80) REVERT: B 220 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8317 (tt) REVERT: B 328 MET cc_start: 0.6377 (tmm) cc_final: 0.5458 (tmm) REVERT: E 406 MET cc_start: 0.8264 (tmm) cc_final: 0.7557 (ttt) REVERT: E 481 ARG cc_start: 0.7423 (mtm-85) cc_final: 0.7114 (ttm-80) REVERT: E 488 GLN cc_start: 0.7952 (tt0) cc_final: 0.7695 (tt0) REVERT: E 511 ARG cc_start: 0.7739 (ttm170) cc_final: 0.6482 (ttm-80) REVERT: E 585 GLN cc_start: 0.7309 (tm-30) cc_final: 0.6950 (pp30) REVERT: E 588 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6852 (mt0) REVERT: E 640 THR cc_start: 0.7836 (t) cc_final: 0.7594 (m) REVERT: E 682 GLU cc_start: 0.7449 (tp30) cc_final: 0.7235 (tp30) REVERT: E 712 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7126 (mtm-85) REVERT: E 781 TYR cc_start: 0.7686 (m-80) cc_final: 0.7275 (m-80) REVERT: E 996 THR cc_start: 0.7759 (m) cc_final: 0.7447 (p) REVERT: E 1132 MET cc_start: 0.8036 (tmt) cc_final: 0.7824 (ttp) outliers start: 33 outliers final: 28 residues processed: 188 average time/residue: 0.5785 time to fit residues: 117.2414 Evaluate side-chains 200 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 VAL 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 660 SER Chi-restraints excluded: chain E residue 687 CYS Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 939 VAL Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 995 MET Chi-restraints excluded: chain E residue 1008 LEU 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 Chi-restraints excluded: chain E residue 1173 ARG 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: 0.6980 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 847 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.189762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.156804 restraints weight = 15968.171| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.87 r_work: 0.3888 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12359 Z= 0.154 Angle : 0.616 10.725 17088 Z= 0.314 Chirality : 0.040 0.157 1970 Planarity : 0.005 0.048 1966 Dihedral : 18.431 99.401 2234 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.20 % Allowed : 20.29 % Favored : 76.51 % 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 aren not related in a simple way. whole: -0.03 (0.23), residues: 1380 helix: 1.41 (0.20), residues: 700 sheet: -0.49 (0.58), residues: 96 loop : -1.79 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 507 TYR 0.036 0.002 TYR E 468 PHE 0.013 0.001 PHE E 802 TRP 0.011 0.001 TRP E 707 HIS 0.012 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00348 (12359) covalent geometry : angle 0.61562 (17088) hydrogen bonds : bond 0.04668 ( 568) hydrogen bonds : angle 3.85305 ( 1596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4746.85 seconds wall clock time: 81 minutes 10.74 seconds (4870.74 seconds total)