Starting phenix.real_space_refine on Wed May 14 16:34:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8v_42028/05_2025/8u8v_42028.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8v_42028/05_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_42028/05_2025/8u8v_42028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8v_42028/05_2025/8u8v_42028.map" model { file = "/net/cci-nas-00/data/ceres_data/8u8v_42028/05_2025/8u8v_42028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8v_42028/05_2025/8u8v_42028.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP: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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} 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, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 17} 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: 7.28, per 1000 atoms: 0.61 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: 2.95 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 3.81 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: 4.69 Time building geometry restraints manager: 3.41 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: 1.470 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.400 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.240 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (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 TRP 0.017 0.001 TRP A 182 HIS 0.006 0.001 HIS E1052 PHE 0.021 0.002 PHE E 802 TYR 0.026 0.002 TYR E 956 ARG 0.006 0.000 ARG E1007 Details of bonding type rmsd hydrogen bonds : bond 0.19721 ( 568) hydrogen bonds : angle 6.48521 ( 1596) covalent geometry : bond 0.00507 (12359) covalent geometry : angle 0.89069 (17088) *********************** 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 : 1.075 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: 1.2157 time to fit residues: 292.0684 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 : 1.245 ------------------------------------------------------------------------------- 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 121 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN A 346 GLN ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 HIS E 722 GLN E 836 HIS E 893 GLN E 903 ASN E 920 HIS E 945 ASN E 979 GLN E1051 GLN ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1117 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.194107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.160824 restraints weight = 16048.719| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 1.93 r_work: 0.3933 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 12359 Z= 0.186 Angle : 0.655 9.699 17088 Z= 0.343 Chirality : 0.042 0.200 1970 Planarity : 0.006 0.058 1966 Dihedral : 19.472 103.446 2235 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.93 % Allowed : 11.06 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1380 helix: 0.63 (0.20), residues: 695 sheet: -0.81 (0.54), residues: 95 loop : -1.78 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E1070 HIS 0.006 0.001 HIS E1131 PHE 0.017 0.002 PHE E 802 TYR 0.021 0.002 TYR E 468 ARG 0.010 0.001 ARG E1048 Details of bonding type rmsd hydrogen bonds : bond 0.05529 ( 568) hydrogen bonds : angle 4.23400 ( 1596) covalent geometry : bond 0.00418 (12359) covalent geometry : angle 0.65495 (17088) *********************** 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 217 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 1.098 Fit side-chains REVERT: A 258 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.5598 (t80) REVERT: B 164 LEU cc_start: 0.7938 (mt) cc_final: 0.7729 (mp) REVERT: B 189 LEU cc_start: 0.7101 (tt) cc_final: 0.6744 (mm) REVERT: E 263 MET cc_start: 0.2310 (ptp) cc_final: 0.0722 (tpp) REVERT: E 406 MET cc_start: 0.8263 (tmm) cc_final: 0.7653 (ttt) REVERT: E 481 ARG cc_start: 0.7397 (mtm-85) cc_final: 0.7145 (ttm170) REVERT: E 585 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7097 (pp30) REVERT: E 615 VAL cc_start: 0.8479 (t) cc_final: 0.8154 (p) REVERT: E 640 THR cc_start: 0.7868 (t) cc_final: 0.7615 (m) REVERT: E 671 MET cc_start: 0.8111 (mmt) cc_final: 0.7704 (mtp) REVERT: E 682 GLU cc_start: 0.7497 (tp30) cc_final: 0.7272 (tp30) REVERT: E 854 ARG cc_start: 0.7821 (mtp85) cc_final: 0.7597 (mtp85) REVERT: E 955 VAL cc_start: 0.8200 (m) cc_final: 0.7969 (p) REVERT: E 996 THR cc_start: 0.7911 (m) cc_final: 0.7589 (p) REVERT: E 1039 SER cc_start: 0.3484 (OUTLIER) cc_final: 0.3107 (p) outliers start: 32 outliers final: 13 residues processed: 197 average time/residue: 1.3464 time to fit residues: 286.1691 Evaluate side-chains 184 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 468 TYR Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 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 47 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 105 optimal weight: 0.4980 chunk 134 optimal weight: 0.0070 chunk 20 optimal weight: 0.0770 chunk 85 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 E1063 HIS E1117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.193574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.160569 restraints weight = 16212.840| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 1.88 r_work: 0.3938 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12359 Z= 0.146 Angle : 0.590 9.721 17088 Z= 0.308 Chirality : 0.039 0.159 1970 Planarity : 0.005 0.051 1966 Dihedral : 19.202 104.168 2234 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.93 % Allowed : 14.08 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.22), residues: 1380 helix: 0.97 (0.20), residues: 698 sheet: -0.59 (0.54), residues: 98 loop : -1.68 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 707 HIS 0.006 0.001 HIS E1131 PHE 0.015 0.001 PHE E 802 TYR 0.021 0.002 TYR E 468 ARG 0.008 0.000 ARG E 507 Details of bonding type rmsd hydrogen bonds : bond 0.04791 ( 568) hydrogen bonds : angle 3.95037 ( 1596) covalent geometry : bond 0.00318 (12359) covalent geometry : angle 0.59040 (17088) *********************** 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 222 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.5539 (t80) REVERT: B 164 LEU cc_start: 0.7916 (mt) cc_final: 0.7703 (mp) REVERT: B 189 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6749 (mm) REVERT: B 203 MET cc_start: 0.8089 (mmm) cc_final: 0.7859 (mmt) REVERT: B 328 MET cc_start: 0.6270 (tmm) cc_final: 0.5361 (tmm) REVERT: E 406 MET cc_start: 0.8291 (tmm) cc_final: 0.7626 (ttt) REVERT: E 481 ARG cc_start: 0.7374 (mtm-85) cc_final: 0.7138 (ttm170) REVERT: E 585 GLN cc_start: 0.7510 (tm-30) cc_final: 0.7059 (pp30) REVERT: E 588 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6997 (mt0) REVERT: E 640 THR cc_start: 0.7828 (t) cc_final: 0.7577 (m) REVERT: E 671 MET cc_start: 0.8156 (mmt) cc_final: 0.7901 (mtp) REVERT: E 682 GLU cc_start: 0.7473 (tp30) cc_final: 0.7250 (tp30) REVERT: E 712 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7242 (mtm-85) REVERT: E 955 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.8020 (p) REVERT: E 996 THR cc_start: 0.7860 (m) cc_final: 0.7585 (p) outliers start: 43 outliers final: 14 residues processed: 197 average time/residue: 1.3508 time to fit residues: 285.6744 Evaluate side-chains 192 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 173 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain E residue 402 LYS 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 712 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 1032 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 0 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 0.0570 chunk 44 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- 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 847 ASN 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 = 0.4383 r_free = 0.4383 target = 0.191425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.158796 restraints weight = 15944.782| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.03 r_work: 0.3889 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12359 Z= 0.173 Angle : 0.625 9.333 17088 Z= 0.327 Chirality : 0.041 0.174 1970 Planarity : 0.005 0.048 1966 Dihedral : 19.098 102.971 2234 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.93 % Allowed : 16.64 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1380 helix: 1.10 (0.20), residues: 689 sheet: -0.56 (0.57), residues: 95 loop : -1.70 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 194 HIS 0.008 0.001 HIS E1131 PHE 0.015 0.002 PHE E 721 TYR 0.032 0.002 TYR E 468 ARG 0.008 0.000 ARG E 507 Details of bonding type rmsd hydrogen bonds : bond 0.05185 ( 568) hydrogen bonds : angle 3.99760 ( 1596) covalent geometry : bond 0.00387 (12359) covalent geometry : angle 0.62479 (17088) *********************** 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 213 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 213 LEU cc_start: 0.7936 (tt) cc_final: 0.7660 (tp) REVERT: A 258 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.5711 (t80) REVERT: B 164 LEU cc_start: 0.7940 (mt) cc_final: 0.7737 (mp) REVERT: B 189 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6778 (mm) REVERT: B 328 MET cc_start: 0.6337 (tmm) cc_final: 0.5434 (tmm) REVERT: E 406 MET cc_start: 0.8324 (tmm) cc_final: 0.7654 (ttt) REVERT: E 481 ARG cc_start: 0.7430 (mtm-85) cc_final: 0.7185 (ttm170) REVERT: E 511 ARG cc_start: 0.7760 (ttm170) cc_final: 0.6479 (ttm-80) REVERT: E 585 GLN cc_start: 0.7521 (tm-30) cc_final: 0.7067 (pp30) REVERT: E 640 THR cc_start: 0.7876 (t) cc_final: 0.7632 (m) REVERT: E 671 MET cc_start: 0.8165 (mmt) cc_final: 0.7943 (mtp) REVERT: E 682 GLU cc_start: 0.7506 (tp30) cc_final: 0.7287 (tp30) REVERT: E 712 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7313 (mtm-85) REVERT: E 866 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7084 (mm-30) REVERT: E 996 THR cc_start: 0.7874 (m) cc_final: 0.7551 (p) outliers start: 43 outliers final: 20 residues processed: 189 average time/residue: 1.2472 time to fit residues: 255.2434 Evaluate side-chains 191 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 402 LYS 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 532 LYS 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 731 VAL Chi-restraints excluded: chain E residue 778 GLU Chi-restraints excluded: chain E residue 866 GLU Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 1031 TYR Chi-restraints excluded: chain E residue 1032 LEU Chi-restraints excluded: chain E residue 1068 VAL Chi-restraints excluded: chain E residue 1069 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 5 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN E 488 GLN ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 HIS E1117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.188106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.154041 restraints weight = 15818.050| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.94 r_work: 0.3855 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12359 Z= 0.216 Angle : 0.676 11.702 17088 Z= 0.349 Chirality : 0.043 0.169 1970 Planarity : 0.006 0.052 1966 Dihedral : 18.975 100.597 2234 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.48 % Allowed : 16.91 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1380 helix: 0.98 (0.20), residues: 688 sheet: -0.81 (0.61), residues: 85 loop : -1.89 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 707 HIS 0.008 0.002 HIS E 624 PHE 0.017 0.002 PHE E1119 TYR 0.020 0.002 TYR A 258 ARG 0.010 0.001 ARG E 507 Details of bonding type rmsd hydrogen bonds : bond 0.06000 ( 568) hydrogen bonds : angle 4.11478 ( 1596) covalent geometry : bond 0.00500 (12359) covalent geometry : angle 0.67564 (17088) *********************** 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 227 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 1.225 Fit side-chains REVERT: A 258 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.5892 (t80) REVERT: B 189 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6782 (mm) REVERT: B 220 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8324 (tt) REVERT: B 256 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7927 (mtp) REVERT: B 328 MET cc_start: 0.6422 (tmm) cc_final: 0.5482 (tmm) REVERT: E 226 LEU cc_start: 0.5402 (mm) cc_final: 0.5182 (mt) REVERT: E 481 ARG cc_start: 0.7340 (mtm-85) cc_final: 0.7103 (ttm170) REVERT: E 511 ARG cc_start: 0.7709 (ttm170) cc_final: 0.6438 (ttm-80) REVERT: E 536 LEU cc_start: 0.8592 (tp) cc_final: 0.8362 (tt) REVERT: E 585 GLN cc_start: 0.7509 (tm-30) cc_final: 0.7077 (pp30) REVERT: E 588 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7001 (mt0) REVERT: E 640 THR cc_start: 0.7940 (t) cc_final: 0.7662 (m) REVERT: E 671 MET cc_start: 0.8250 (mmt) cc_final: 0.8003 (mtp) REVERT: E 682 GLU cc_start: 0.7439 (tp30) cc_final: 0.7217 (tp30) REVERT: E 712 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7306 (mtm-85) REVERT: E 996 THR cc_start: 0.7915 (m) cc_final: 0.7532 (p) outliers start: 49 outliers final: 23 residues processed: 202 average time/residue: 1.1900 time to fit residues: 260.8585 Evaluate side-chains 201 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 256 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 529 HIS Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 588 GLN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 687 CYS Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 731 VAL Chi-restraints excluded: chain E residue 778 GLU 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 1069 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 141 optimal weight: 10.0000 chunk 111 optimal weight: 0.0470 chunk 53 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 488 GLN ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.190263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.157325 restraints weight = 16050.637| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.87 r_work: 0.3895 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12359 Z= 0.140 Angle : 0.589 10.984 17088 Z= 0.308 Chirality : 0.039 0.222 1970 Planarity : 0.005 0.048 1966 Dihedral : 18.804 101.277 2234 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.84 % Allowed : 18.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.23), residues: 1380 helix: 1.24 (0.20), residues: 693 sheet: -0.49 (0.58), residues: 96 loop : -1.80 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 707 HIS 0.004 0.001 HIS E1131 PHE 0.015 0.001 PHE E 802 TYR 0.012 0.001 TYR E1004 ARG 0.009 0.000 ARG E 507 Details of bonding type rmsd hydrogen bonds : bond 0.04646 ( 568) hydrogen bonds : angle 3.92301 ( 1596) covalent geometry : bond 0.00303 (12359) covalent geometry : angle 0.58856 (17088) *********************** 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 215 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 213 LEU cc_start: 0.7929 (tt) cc_final: 0.7681 (tp) REVERT: A 258 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.5649 (t80) REVERT: B 189 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6849 (mm) REVERT: B 220 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8301 (tt) REVERT: B 256 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7913 (mtp) REVERT: B 328 MET cc_start: 0.6357 (tmm) cc_final: 0.5429 (tmm) REVERT: E 375 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7484 (ttm110) REVERT: E 406 MET cc_start: 0.8316 (tmm) cc_final: 0.7623 (ttt) REVERT: E 481 ARG cc_start: 0.7376 (mtm-85) cc_final: 0.7075 (ttm-80) REVERT: E 488 GLN cc_start: 0.7880 (tt0) cc_final: 0.7627 (tt0) REVERT: E 511 ARG cc_start: 0.7740 (ttm170) cc_final: 0.6498 (ttm-80) REVERT: E 585 GLN cc_start: 0.7383 (tm-30) cc_final: 0.6994 (pp30) REVERT: E 588 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6924 (mt0) REVERT: E 640 THR cc_start: 0.7833 (t) cc_final: 0.7591 (m) REVERT: E 671 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7868 (mtp) REVERT: E 682 GLU cc_start: 0.7407 (tp30) cc_final: 0.7182 (tp30) REVERT: E 712 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7197 (mtm-85) REVERT: E 996 THR cc_start: 0.7824 (m) cc_final: 0.7489 (p) outliers start: 42 outliers final: 21 residues processed: 194 average time/residue: 1.2259 time to fit residues: 257.9764 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 : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 256 MET 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 578 LEU Chi-restraints excluded: chain E residue 588 GLN Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 671 MET Chi-restraints excluded: chain E residue 687 CYS Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 791 ASP 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 121 optimal weight: 0.0670 chunk 64 optimal weight: 0.1980 chunk 132 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 55 optimal weight: 0.0980 overall best weight: 0.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 HIS E 512 HIS E 847 ASN E1117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.193515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.160893 restraints weight = 16169.153| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 1.91 r_work: 0.3936 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12359 Z= 0.113 Angle : 0.547 9.684 17088 Z= 0.285 Chirality : 0.037 0.167 1970 Planarity : 0.005 0.064 1966 Dihedral : 18.567 97.658 2234 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.47 % Allowed : 19.01 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 1380 helix: 1.55 (0.21), residues: 696 sheet: -0.37 (0.57), residues: 98 loop : -1.69 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 567 HIS 0.006 0.001 HIS E 249 PHE 0.021 0.001 PHE B 228 TYR 0.010 0.001 TYR E1004 ARG 0.009 0.000 ARG E 507 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 568) hydrogen bonds : angle 3.67598 ( 1596) covalent geometry : bond 0.00234 (12359) covalent geometry : angle 0.54717 (17088) *********************** 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 209 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 1.196 Fit side-chains REVERT: A 258 TYR cc_start: 0.6956 (OUTLIER) cc_final: 0.5455 (t80) REVERT: B 220 ILE cc_start: 0.8653 (mt) cc_final: 0.8306 (tt) REVERT: B 256 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7871 (mtp) REVERT: B 328 MET cc_start: 0.6350 (tmm) cc_final: 0.5441 (tmm) REVERT: E 406 MET cc_start: 0.8243 (tmm) cc_final: 0.7565 (ttt) REVERT: E 481 ARG cc_start: 0.7408 (mtm-85) cc_final: 0.7116 (ttm-80) REVERT: E 511 ARG cc_start: 0.7755 (ttm170) cc_final: 0.6516 (ttm-80) REVERT: E 585 GLN cc_start: 0.7340 (tm-30) cc_final: 0.6920 (pp30) REVERT: E 640 THR cc_start: 0.7792 (t) cc_final: 0.7551 (m) REVERT: E 671 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7770 (mtp) REVERT: E 682 GLU cc_start: 0.7427 (tp30) cc_final: 0.7206 (tp30) REVERT: E 712 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7073 (mtm-85) REVERT: E 866 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7205 (mm-30) REVERT: E 937 ASP cc_start: 0.6726 (m-30) cc_final: 0.6280 (m-30) REVERT: E 996 THR cc_start: 0.7786 (m) cc_final: 0.7427 (p) REVERT: E 1169 GLU cc_start: 0.7823 (tp30) cc_final: 0.7609 (tp30) outliers start: 38 outliers final: 13 residues processed: 188 average time/residue: 1.2984 time to fit residues: 263.8966 Evaluate side-chains 182 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 671 MET Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 866 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 488 GLN E 617 GLN E 847 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.189404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.155733 restraints weight = 16094.026| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.91 r_work: 0.3871 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12359 Z= 0.182 Angle : 0.642 11.104 17088 Z= 0.327 Chirality : 0.041 0.158 1970 Planarity : 0.005 0.048 1966 Dihedral : 18.566 98.516 2234 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.74 % Allowed : 20.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.23), residues: 1380 helix: 1.44 (0.20), residues: 691 sheet: -0.57 (0.63), residues: 86 loop : -1.80 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 707 HIS 0.007 0.001 HIS E 920 PHE 0.014 0.001 PHE E 802 TYR 0.017 0.002 TYR A 258 ARG 0.011 0.000 ARG E 507 Details of bonding type rmsd hydrogen bonds : bond 0.05185 ( 568) hydrogen bonds : angle 3.89666 ( 1596) covalent geometry : bond 0.00420 (12359) covalent geometry : angle 0.64209 (17088) *********************** 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 199 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.244 Fit side-chains REVERT: A 213 LEU cc_start: 0.7932 (tt) cc_final: 0.7681 (tp) REVERT: A 258 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.5773 (t80) REVERT: B 220 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8329 (tt) REVERT: B 256 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7978 (mtp) REVERT: B 328 MET cc_start: 0.6401 (tmm) cc_final: 0.5483 (tmm) REVERT: E 406 MET cc_start: 0.8272 (tmm) cc_final: 0.7619 (ttt) REVERT: E 481 ARG cc_start: 0.7403 (mtm-85) cc_final: 0.7099 (ttm-80) REVERT: E 488 GLN cc_start: 0.7934 (tt0) cc_final: 0.7666 (tt0) REVERT: E 511 ARG cc_start: 0.7779 (ttm170) cc_final: 0.6558 (ttm-80) REVERT: E 585 GLN cc_start: 0.7312 (tm-30) cc_final: 0.6933 (pp30) REVERT: E 588 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6914 (mt0) REVERT: E 640 THR cc_start: 0.7872 (t) cc_final: 0.7640 (m) REVERT: E 671 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7963 (mtp) REVERT: E 682 GLU cc_start: 0.7440 (tp30) cc_final: 0.7220 (tp30) REVERT: E 712 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7215 (mtm-85) REVERT: E 781 TYR cc_start: 0.7666 (m-80) cc_final: 0.7258 (m-80) REVERT: E 866 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7152 (mm-30) REVERT: E 996 THR cc_start: 0.7852 (m) cc_final: 0.7532 (p) outliers start: 30 outliers final: 15 residues processed: 183 average time/residue: 1.2363 time to fit residues: 245.1037 Evaluate side-chains 188 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 258 TYR 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 256 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 588 GLN Chi-restraints excluded: chain E residue 671 MET Chi-restraints excluded: chain E residue 687 CYS Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 778 GLU Chi-restraints excluded: chain E residue 866 GLU Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 1008 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 82 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 54 optimal weight: 0.0040 chunk 26 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 = 0.4385 r_free = 0.4385 target = 0.191627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.158588 restraints weight = 15957.661| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.90 r_work: 0.3906 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12359 Z= 0.129 Angle : 0.590 10.434 17088 Z= 0.301 Chirality : 0.038 0.156 1970 Planarity : 0.005 0.047 1966 Dihedral : 18.457 98.388 2234 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.38 % Allowed : 20.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.23), residues: 1380 helix: 1.50 (0.20), residues: 696 sheet: -0.42 (0.57), residues: 101 loop : -1.71 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 707 HIS 0.007 0.001 HIS E 920 PHE 0.014 0.001 PHE E 802 TYR 0.024 0.001 TYR E 468 ARG 0.009 0.000 ARG E 507 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 568) hydrogen bonds : angle 3.79171 ( 1596) covalent geometry : bond 0.00282 (12359) covalent geometry : angle 0.59048 (17088) *********************** 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 191 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.254 Fit side-chains REVERT: A 213 LEU cc_start: 0.7892 (tt) cc_final: 0.7680 (tt) REVERT: A 258 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.5549 (t80) REVERT: A 335 GLN cc_start: 0.6601 (OUTLIER) cc_final: 0.5126 (pm20) REVERT: B 220 ILE cc_start: 0.8718 (mt) cc_final: 0.8338 (tt) REVERT: B 256 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7901 (mtp) REVERT: B 328 MET cc_start: 0.6370 (tmm) cc_final: 0.5443 (tmm) REVERT: E 375 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7452 (ttm110) REVERT: E 406 MET cc_start: 0.8259 (tmm) cc_final: 0.7529 (ttt) REVERT: E 468 TYR cc_start: 0.7172 (t80) cc_final: 0.6947 (t80) REVERT: E 481 ARG cc_start: 0.7426 (mtm-85) cc_final: 0.7129 (ttm-80) REVERT: E 488 GLN cc_start: 0.7952 (tt0) cc_final: 0.7696 (tt0) REVERT: E 511 ARG cc_start: 0.7760 (ttm170) cc_final: 0.6495 (ttm-80) REVERT: E 585 GLN cc_start: 0.7299 (tm-30) cc_final: 0.6922 (pp30) REVERT: E 588 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6892 (mt0) REVERT: E 640 THR cc_start: 0.7838 (t) cc_final: 0.7599 (m) REVERT: E 671 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7808 (mtp) REVERT: E 682 GLU cc_start: 0.7410 (tp30) cc_final: 0.7190 (tp30) REVERT: E 712 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7159 (mtm-85) REVERT: E 781 TYR cc_start: 0.7647 (m-80) cc_final: 0.7269 (m-80) REVERT: E 866 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7214 (mm-30) REVERT: E 996 THR cc_start: 0.7751 (m) cc_final: 0.7421 (p) outliers start: 26 outliers final: 16 residues processed: 176 average time/residue: 1.3025 time to fit residues: 247.5887 Evaluate side-chains 188 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 529 HIS Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 588 GLN Chi-restraints excluded: chain E residue 671 MET Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 866 GLU 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 131 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.4356 r_free = 0.4356 target = 0.189137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.155456 restraints weight = 15841.103| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.88 r_work: 0.3870 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12359 Z= 0.178 Angle : 0.651 11.758 17088 Z= 0.329 Chirality : 0.041 0.153 1970 Planarity : 0.005 0.049 1966 Dihedral : 18.462 98.907 2234 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.65 % Allowed : 21.12 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.23), residues: 1380 helix: 1.39 (0.20), residues: 691 sheet: -0.52 (0.59), residues: 96 loop : -1.83 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E1053 HIS 0.011 0.001 HIS E 920 PHE 0.013 0.001 PHE E 802 TYR 0.017 0.002 TYR A 258 ARG 0.007 0.000 ARG E 507 Details of bonding type rmsd hydrogen bonds : bond 0.05244 ( 568) hydrogen bonds : angle 3.96137 ( 1596) covalent geometry : bond 0.00408 (12359) covalent geometry : angle 0.65063 (17088) ********************** 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 204 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 1.238 Fit side-chains REVERT: A 213 LEU cc_start: 0.7940 (tt) cc_final: 0.7688 (tp) REVERT: A 258 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.5772 (t80) REVERT: A 335 GLN cc_start: 0.6526 (OUTLIER) cc_final: 0.5040 (pm20) REVERT: B 220 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8322 (tt) REVERT: B 256 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8010 (mtp) REVERT: B 328 MET cc_start: 0.6375 (tmm) cc_final: 0.5466 (tmm) REVERT: E 406 MET cc_start: 0.8272 (tmm) cc_final: 0.7649 (ttt) REVERT: E 481 ARG cc_start: 0.7384 (mtm-85) cc_final: 0.7073 (ttm-80) REVERT: E 488 GLN cc_start: 0.7928 (tt0) cc_final: 0.7655 (tt0) REVERT: E 511 ARG cc_start: 0.7776 (ttm170) cc_final: 0.6562 (ttm-80) REVERT: E 585 GLN cc_start: 0.7299 (tm-30) cc_final: 0.6944 (pp30) REVERT: E 588 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6875 (mt0) REVERT: E 640 THR cc_start: 0.7874 (t) cc_final: 0.7625 (m) REVERT: E 671 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7953 (mtp) REVERT: E 682 GLU cc_start: 0.7395 (tp30) cc_final: 0.7173 (tp30) REVERT: E 712 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7175 (mtm-85) REVERT: E 781 TYR cc_start: 0.7676 (m-80) cc_final: 0.7228 (m-80) REVERT: E 854 ARG cc_start: 0.7725 (mtp180) cc_final: 0.7523 (mmt-90) REVERT: E 866 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7145 (mm-30) REVERT: E 996 THR cc_start: 0.7842 (m) cc_final: 0.7524 (p) outliers start: 29 outliers final: 17 residues processed: 189 average time/residue: 1.3275 time to fit residues: 271.8984 Evaluate side-chains 199 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 335 GLN 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 256 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 588 GLN Chi-restraints excluded: chain E residue 671 MET Chi-restraints excluded: chain E residue 687 CYS Chi-restraints excluded: chain E residue 712 ARG Chi-restraints excluded: chain E residue 731 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 866 GLU 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 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 142 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4368 r_free = 0.4368 target = 0.190173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.156784 restraints weight = 15877.060| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.88 r_work: 0.3886 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12359 Z= 0.148 Angle : 0.611 10.864 17088 Z= 0.311 Chirality : 0.039 0.160 1970 Planarity : 0.005 0.048 1966 Dihedral : 18.401 99.223 2234 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.65 % Allowed : 21.02 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.23), residues: 1380 helix: 1.43 (0.20), residues: 695 sheet: -0.60 (0.58), residues: 98 loop : -1.76 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 707 HIS 0.011 0.001 HIS E 920 PHE 0.014 0.001 PHE E 802 TYR 0.012 0.002 TYR E1004 ARG 0.008 0.000 ARG E 507 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 568) hydrogen bonds : angle 3.88929 ( 1596) covalent geometry : bond 0.00332 (12359) covalent geometry : angle 0.61097 (17088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10578.73 seconds wall clock time: 181 minutes 53.52 seconds (10913.52 seconds total)