Starting phenix.real_space_refine on Tue May 20 03:57:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9khz_62360/05_2025/9khz_62360.cif Found real_map, /net/cci-nas-00/data/ceres_data/9khz_62360/05_2025/9khz_62360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9khz_62360/05_2025/9khz_62360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9khz_62360/05_2025/9khz_62360.map" model { file = "/net/cci-nas-00/data/ceres_data/9khz_62360/05_2025/9khz_62360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9khz_62360/05_2025/9khz_62360.cif" } resolution = 3.03 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= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 48 5.16 5 C 12231 2.51 5 N 3371 2.21 5 O 3756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19432 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9502 Classifications: {'peptide': 1175} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1141} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 9439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 9439 Classifications: {'peptide': 1168} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1134} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 218 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "D" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 219 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.10, per 1000 atoms: 0.57 Number of scatterers: 19432 At special positions: 0 Unit cell: (130.353, 126.044, 132.508, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 26 15.00 O 3756 8.00 N 3371 7.00 C 12231 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: 4.53 Conformation dependent library (CDL) restraints added in 2.5 seconds 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4472 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 26 sheets defined 53.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 removed outlier: 3.843A pdb=" N GLU A 7 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HIS A 10 " --> pdb=" O GLU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 37 removed outlier: 3.748A pdb=" N ILE A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 78 Processing helix chain 'A' and resid 94 through 111 removed outlier: 3.567A pdb=" N VAL A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 132 removed outlier: 3.537A pdb=" N ILE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.567A pdb=" N ALA A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 206 removed outlier: 3.786A pdb=" N SER A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.518A pdb=" N ALA A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 259 through 264 removed outlier: 3.722A pdb=" N LEU A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 293 through 307 removed outlier: 4.550A pdb=" N ASP A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.753A pdb=" N PHE A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 401 through 431 Processing helix chain 'A' and resid 445 through 459 removed outlier: 4.377A pdb=" N GLN A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.509A pdb=" N ASP A 473 " --> pdb=" O TYR A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.736A pdb=" N GLY A 536 " --> pdb=" O MET A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 565 Processing helix chain 'A' and resid 573 through 587 removed outlier: 4.118A pdb=" N GLN A 577 " --> pdb=" O ARG A 573 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 removed outlier: 3.692A pdb=" N LEU A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 628 Processing helix chain 'A' and resid 637 through 657 removed outlier: 3.761A pdb=" N LEU A 647 " --> pdb=" O TRP A 643 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 693 removed outlier: 4.312A pdb=" N PHE A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 711 Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.543A pdb=" N SER A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 737 removed outlier: 3.971A pdb=" N GLY A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 733 through 737' Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 789 through 806 Processing helix chain 'A' and resid 811 through 825 Processing helix chain 'A' and resid 827 through 837 Processing helix chain 'A' and resid 839 through 855 removed outlier: 3.631A pdb=" N SER A 843 " --> pdb=" O SER A 839 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 847 " --> pdb=" O SER A 843 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 854 " --> pdb=" O GLU A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 858 No H-bonds generated for 'chain 'A' and resid 856 through 858' Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 889 through 901 removed outlier: 3.831A pdb=" N LYS A 898 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 899 " --> pdb=" O LEU A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 921 removed outlier: 3.799A pdb=" N ARG A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 916 " --> pdb=" O VAL A 912 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN A 917 " --> pdb=" O ARG A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 938 removed outlier: 3.651A pdb=" N ALA A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 960 Processing helix chain 'A' and resid 992 through 996 removed outlier: 3.979A pdb=" N PHE A 996 " --> pdb=" O PRO A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1021 removed outlier: 4.231A pdb=" N ASN A1021 " --> pdb=" O THR A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1029 Processing helix chain 'A' and resid 1045 through 1051 Processing helix chain 'A' and resid 1052 through 1068 removed outlier: 3.501A pdb=" N GLY A1058 " --> pdb=" O LYS A1054 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A1059 " --> pdb=" O GLY A1055 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A1068 " --> pdb=" O ALA A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1127 removed outlier: 4.135A pdb=" N VAL A1122 " --> pdb=" O LYS A1118 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1190 removed outlier: 4.135A pdb=" N SER A1190 " --> pdb=" O TRP A1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 20 through 38 removed outlier: 3.609A pdb=" N VAL B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 30 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS B 33 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 77 Processing helix chain 'B' and resid 94 through 112 removed outlier: 3.599A pdb=" N GLU B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 131 Processing helix chain 'B' and resid 137 through 143 Processing helix chain 'B' and resid 146 through 157 Processing helix chain 'B' and resid 158 through 161 removed outlier: 3.944A pdb=" N ALA B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 158 through 161' Processing helix chain 'B' and resid 162 through 178 removed outlier: 3.700A pdb=" N HIS B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 209 removed outlier: 4.120A pdb=" N SER B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 227 through 235 removed outlier: 3.853A pdb=" N LYS B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 232 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 276 through 286 Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 312 through 316 removed outlier: 3.793A pdb=" N ASP B 316 " --> pdb=" O PRO B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 322 removed outlier: 3.765A pdb=" N LEU B 321 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 317 through 322' Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 401 through 434 removed outlier: 4.057A pdb=" N GLY B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 459 removed outlier: 4.013A pdb=" N GLN B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 453 " --> pdb=" O GLN B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 464 through 470 Processing helix chain 'B' and resid 493 through 497 removed outlier: 3.763A pdb=" N HIS B 496 " --> pdb=" O SER B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 536 Processing helix chain 'B' and resid 558 through 565 Processing helix chain 'B' and resid 572 through 587 Processing helix chain 'B' and resid 588 through 593 removed outlier: 3.871A pdb=" N ASN B 592 " --> pdb=" O ASN B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 616 removed outlier: 3.660A pdb=" N LEU B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 629 removed outlier: 3.672A pdb=" N ILE B 625 " --> pdb=" O SER B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 657 removed outlier: 3.559A pdb=" N SER B 642 " --> pdb=" O ALA B 638 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 647 " --> pdb=" O TRP B 643 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 650 " --> pdb=" O LYS B 646 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 653 " --> pdb=" O ALA B 649 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 693 removed outlier: 3.837A pdb=" N PHE B 681 " --> pdb=" O ASN B 677 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 723 removed outlier: 3.634A pdb=" N GLU B 715 " --> pdb=" O VAL B 711 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B 716 " --> pdb=" O GLY B 712 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 717 " --> pdb=" O TYR B 713 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 720 " --> pdb=" O ILE B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 737 Processing helix chain 'B' and resid 789 through 808 removed outlier: 3.616A pdb=" N CYS B 796 " --> pdb=" O ALA B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 825 removed outlier: 3.509A pdb=" N ASN B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 837 removed outlier: 3.649A pdb=" N GLN B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 856 removed outlier: 3.820A pdb=" N SER B 843 " --> pdb=" O SER B 839 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 847 " --> pdb=" O SER B 843 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 850 " --> pdb=" O ARG B 846 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 880 removed outlier: 3.527A pdb=" N GLU B 880 " --> pdb=" O GLU B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 889 through 901 removed outlier: 3.769A pdb=" N ALA B 894 " --> pdb=" O HIS B 890 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 895 " --> pdb=" O GLU B 891 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 898 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA B 899 " --> pdb=" O LEU B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 936 removed outlier: 3.516A pdb=" N LEU B 915 " --> pdb=" O ALA B 911 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 917 " --> pdb=" O ARG B 913 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 931 " --> pdb=" O MET B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 960 Processing helix chain 'B' and resid 992 through 996 removed outlier: 3.681A pdb=" N SER B 995 " --> pdb=" O ASP B 992 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE B 996 " --> pdb=" O PRO B 993 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 992 through 996' Processing helix chain 'B' and resid 1000 through 1002 No H-bonds generated for 'chain 'B' and resid 1000 through 1002' Processing helix chain 'B' and resid 1009 through 1014 removed outlier: 3.822A pdb=" N CYS B1013 " --> pdb=" O SER B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1021 removed outlier: 3.561A pdb=" N LEU B1018 " --> pdb=" O SER B1014 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN B1021 " --> pdb=" O THR B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1032 removed outlier: 3.793A pdb=" N TRP B1027 " --> pdb=" O TYR B1023 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B1029 " --> pdb=" O ARG B1025 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B1030 " --> pdb=" O PRO B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1051 Processing helix chain 'B' and resid 1053 through 1068 removed outlier: 3.655A pdb=" N GLU B1059 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B1063 " --> pdb=" O GLU B1059 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA B1068 " --> pdb=" O ALA B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1127 removed outlier: 3.501A pdb=" N LYS B1118 " --> pdb=" O GLY B1114 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU B1125 " --> pdb=" O LEU B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1155 through 1159 Processing helix chain 'B' and resid 1176 through 1190 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 47 removed outlier: 6.710A pdb=" N LEU A 88 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU A 242 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N TYR A 90 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292 removed outlier: 3.562A pdb=" N ALA A 505 " --> pdb=" O ASN A 515 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 354 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.155A pdb=" N ALA A 341 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE A 385 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASN A 343 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N SER A 387 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 596 through 600 removed outlier: 3.514A pdb=" N VAL A 870 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 773 " --> pdb=" O TYR A 662 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 775 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N MET A 663 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N SER A 731 " --> pdb=" O MET A 663 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N SER A 665 " --> pdb=" O SER A 731 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 728 " --> pdb=" O LYS A 698 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 744 through 745 Processing sheet with id=AA8, first strand: chain 'A' and resid 755 through 757 Processing sheet with id=AA9, first strand: chain 'A' and resid 962 through 963 Processing sheet with id=AB1, first strand: chain 'A' and resid 984 through 985 Processing sheet with id=AB2, first strand: chain 'A' and resid 1074 through 1075 removed outlier: 3.532A pdb=" N ASN A1086 " --> pdb=" O LEU A1099 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL A1134 " --> pdb=" O TRP A1098 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP A1100 " --> pdb=" O VAL A1134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1137 through 1138 Processing sheet with id=AB4, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.526A pdb=" N LEU B 242 " --> pdb=" O TYR B 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AB7, first strand: chain 'B' and resid 251 through 252 Processing sheet with id=AB8, first strand: chain 'B' and resid 291 through 292 removed outlier: 3.638A pdb=" N ALA B 505 " --> pdb=" O ASN B 515 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 354 " --> pdb=" O VAL B 504 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 341 through 344 removed outlier: 5.951A pdb=" N ALA B 341 " --> pdb=" O ASN B 383 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE B 385 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASN B 343 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N SER B 387 " --> pdb=" O ASN B 343 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 382 " --> pdb=" O ASP B 377 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 595 through 601 removed outlier: 3.692A pdb=" N ILE B 774 " --> pdb=" O LEU B 867 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET B 663 " --> pdb=" O VAL B 729 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N SER B 731 " --> pdb=" O MET B 663 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N SER B 665 " --> pdb=" O SER B 731 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 730 " --> pdb=" O PHE B 700 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 743 through 745 removed outlier: 3.621A pdb=" N TYR B 744 " --> pdb=" O SER B 769 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 755 through 756 Processing sheet with id=AC4, first strand: chain 'B' and resid 974 through 976 Processing sheet with id=AC5, first strand: chain 'B' and resid 997 through 998 Processing sheet with id=AC6, first strand: chain 'B' and resid 1073 through 1074 Processing sheet with id=AC7, first strand: chain 'B' and resid 1131 through 1132 removed outlier: 6.726A pdb=" N PHE B1131 " --> pdb=" O ILE B1162 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1137 through 1138 866 hydrogen bonds defined for protein. 2469 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.70 Time building geometry restraints manager: 5.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3240 1.31 - 1.44: 5445 1.44 - 1.56: 11046 1.56 - 1.69: 50 1.69 - 1.81: 76 Bond restraints: 19857 Sorted by residual: bond pdb=" CA THR B 56 " pdb=" C THR B 56 " ideal model delta sigma weight residual 1.523 1.427 0.096 1.34e-02 5.57e+03 5.16e+01 bond pdb=" CA LEU B 47 " pdb=" C LEU B 47 " ideal model delta sigma weight residual 1.522 1.476 0.047 8.40e-03 1.42e+04 3.06e+01 bond pdb=" CA ALA A 759 " pdb=" C ALA A 759 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.34e-02 5.57e+03 2.23e+01 bond pdb=" N LEU B 47 " pdb=" CA LEU B 47 " ideal model delta sigma weight residual 1.460 1.403 0.057 1.29e-02 6.01e+03 1.95e+01 bond pdb=" CA TYR B 57 " pdb=" CB TYR B 57 " ideal model delta sigma weight residual 1.530 1.462 0.069 1.69e-02 3.50e+03 1.65e+01 ... (remaining 19852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 26500 2.43 - 4.85: 368 4.85 - 7.28: 50 7.28 - 9.71: 10 9.71 - 12.13: 2 Bond angle restraints: 26930 Sorted by residual: angle pdb=" CA PRO A1128 " pdb=" N PRO A1128 " pdb=" CD PRO A1128 " ideal model delta sigma weight residual 112.00 100.42 11.58 1.40e+00 5.10e-01 6.84e+01 angle pdb=" C THR B 56 " pdb=" CA THR B 56 " pdb=" CB THR B 56 " ideal model delta sigma weight residual 110.42 98.29 12.13 1.99e+00 2.53e-01 3.72e+01 angle pdb=" N LEU A 477 " pdb=" CA LEU A 477 " pdb=" C LEU A 477 " ideal model delta sigma weight residual 113.19 106.27 6.92 1.19e+00 7.06e-01 3.38e+01 angle pdb=" N ASN A 430 " pdb=" CA ASN A 430 " pdb=" C ASN A 430 " ideal model delta sigma weight residual 113.28 106.97 6.31 1.22e+00 6.72e-01 2.68e+01 angle pdb=" C GLU A 437 " pdb=" CA GLU A 437 " pdb=" CB GLU A 437 " ideal model delta sigma weight residual 116.54 110.63 5.91 1.15e+00 7.56e-01 2.64e+01 ... (remaining 26925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 11323 34.20 - 68.41: 544 68.41 - 102.61: 33 102.61 - 136.81: 3 136.81 - 171.02: 5 Dihedral angle restraints: 11908 sinusoidal: 5016 harmonic: 6892 Sorted by residual: dihedral pdb=" CD ARG A 442 " pdb=" NE ARG A 442 " pdb=" CZ ARG A 442 " pdb=" NH1 ARG A 442 " ideal model delta sinusoidal sigma weight residual 0.00 -77.50 77.50 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" C2' ADP B1301 " pdb=" C1' ADP B1301 " pdb=" N9 ADP B1301 " pdb=" C4 ADP B1301 " ideal model delta sinusoidal sigma weight residual 91.55 -74.87 166.42 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" O2A ADP A1301 " pdb=" O3A ADP A1301 " pdb=" PA ADP A1301 " pdb=" PB ADP A1301 " ideal model delta sinusoidal sigma weight residual 300.00 135.05 164.95 1 2.00e+01 2.50e-03 4.72e+01 ... (remaining 11905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2673 0.067 - 0.134: 265 0.134 - 0.202: 21 0.202 - 0.269: 5 0.269 - 0.336: 2 Chirality restraints: 2966 Sorted by residual: chirality pdb=" CB VAL B 761 " pdb=" CA VAL B 761 " pdb=" CG1 VAL B 761 " pdb=" CG2 VAL B 761 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA THR B 51 " pdb=" N THR B 51 " pdb=" C THR B 51 " pdb=" CB THR B 51 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA TYR B 57 " pdb=" N TYR B 57 " pdb=" C TYR B 57 " pdb=" CB TYR B 57 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2963 not shown) Planarity restraints: 3415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 442 " -1.056 9.50e-02 1.11e+02 4.73e-01 1.35e+02 pdb=" NE ARG A 442 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A 442 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 442 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 442 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 586 " 0.513 9.50e-02 1.11e+02 2.30e-01 3.24e+01 pdb=" NE ARG B 586 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG B 586 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 586 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 586 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 884 " -0.080 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO B 885 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO B 885 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO B 885 " -0.063 5.00e-02 4.00e+02 ... (remaining 3412 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 222 2.56 - 3.15: 15675 3.15 - 3.73: 30727 3.73 - 4.32: 43449 4.32 - 4.90: 71218 Nonbonded interactions: 161291 Sorted by model distance: nonbonded pdb=" OG1 THR B 56 " pdb=" N TYR B 57 " model vdw 1.979 3.120 nonbonded pdb=" OG1 THR B 243 " pdb=" OP1 DT D 9 " model vdw 2.022 3.040 nonbonded pdb=" OE1 GLN A 951 " pdb=" OH TYR A1081 " model vdw 2.110 3.040 nonbonded pdb=" OG1 THR B 722 " pdb=" OE1 GLU B 723 " model vdw 2.179 3.040 nonbonded pdb=" OG1 THR B 979 " pdb=" O TYR B 982 " model vdw 2.198 3.040 ... (remaining 161286 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 1 through 77 or resid 83 through 390 or resid 398 through \ 473 or resid 485 through 1190 or resid 1301)) selection = (chain 'B' and (resid 1 through 473 or resid 485 through 763 or resid 766 throug \ h 1190 or resid 1301)) } ncs_group { reference = (chain 'C' and (resid 2 or resid 4 through 12)) selection = (chain 'D' and (resid 1 or resid 3 through 11)) } 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: 1.240 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: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 43.320 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 : 0.004 0.164 19857 Z= 0.235 Angle : 0.695 12.133 26930 Z= 0.393 Chirality : 0.043 0.336 2966 Planarity : 0.010 0.473 3415 Dihedral : 18.785 171.019 7436 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.53 % Favored : 92.04 % Rotamer: Outliers : 0.67 % Allowed : 24.35 % Favored : 74.98 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.03 % 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: -1.93 (0.17), residues: 2325 helix: -0.39 (0.15), residues: 1050 sheet: -2.26 (0.32), residues: 267 loop : -1.89 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B1104 HIS 0.005 0.001 HIS B 134 PHE 0.027 0.001 PHE A 607 TYR 0.015 0.001 TYR B 57 ARG 0.006 0.000 ARG A 972 Details of bonding type rmsd hydrogen bonds : bond 0.26680 ( 866) hydrogen bonds : angle 8.41948 ( 2469) covalent geometry : bond 0.00429 (19857) covalent geometry : angle 0.69480 (26930) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 2.019 Fit side-chains revert: symmetry clash REVERT: A 1130 LYS cc_start: 0.6384 (mttp) cc_final: 0.5106 (tppt) REVERT: B 1186 TRP cc_start: 0.6339 (t-100) cc_final: 0.5938 (t-100) outliers start: 14 outliers final: 3 residues processed: 194 average time/residue: 0.3295 time to fit residues: 96.2467 Evaluate side-chains 170 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain B residue 858 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 5.9990 chunk 178 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 213 optimal weight: 0.7980 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 166 GLN ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN A 668 ASN A1086 ASN B 166 GLN B 426 GLN ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS ** B 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 GLN B 794 GLN B 890 HIS B 935 HIS B 951 GLN B 956 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.176111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.139518 restraints weight = 27836.371| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 3.44 r_work: 0.3472 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 19857 Z= 0.392 Angle : 0.784 11.454 26930 Z= 0.407 Chirality : 0.049 0.179 2966 Planarity : 0.006 0.070 3415 Dihedral : 13.473 179.323 2811 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.65 % Favored : 91.18 % Rotamer: Outliers : 5.63 % Allowed : 21.22 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.83 (0.17), residues: 2325 helix: -0.10 (0.15), residues: 1118 sheet: -2.46 (0.30), residues: 259 loop : -2.14 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B1104 HIS 0.013 0.002 HIS A 238 PHE 0.018 0.003 PHE B 607 TYR 0.018 0.003 TYR B 559 ARG 0.008 0.001 ARG A 972 Details of bonding type rmsd hydrogen bonds : bond 0.06437 ( 866) hydrogen bonds : angle 5.66062 ( 2469) covalent geometry : bond 0.00913 (19857) covalent geometry : angle 0.78423 (26930) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 175 time to evaluate : 2.151 Fit side-chains revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: A 809 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: A 940 GLN cc_start: 0.6856 (mm-40) cc_final: 0.6542 (mm-40) REVERT: A 1028 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.4699 (t80) REVERT: A 1130 LYS cc_start: 0.6554 (mttp) cc_final: 0.5241 (tppt) REVERT: B 205 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7746 (mttp) REVERT: B 238 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.6877 (m-70) REVERT: B 858 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7038 (mtt-85) REVERT: B 890 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.6705 (m90) REVERT: B 978 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6546 (ptp) outliers start: 117 outliers final: 58 residues processed: 274 average time/residue: 0.3209 time to fit residues: 133.9654 Evaluate side-chains 226 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 160 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 809 GLU Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1028 PHE Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1103 TYR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 793 ASN Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 858 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 1006 ASP Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1104 TRP Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1134 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 165 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 168 optimal weight: 0.6980 chunk 8 optimal weight: 0.0770 chunk 159 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 195 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN A 581 ASN A 851 GLN A 951 GLN A 966 GLN A1042 ASN B 124 GLN B 577 GLN B 581 ASN ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.182177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.146096 restraints weight = 27308.718| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 3.18 r_work: 0.3616 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19857 Z= 0.127 Angle : 0.595 9.475 26930 Z= 0.309 Chirality : 0.040 0.182 2966 Planarity : 0.004 0.054 3415 Dihedral : 12.976 177.885 2804 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.18 % Favored : 92.65 % Rotamer: Outliers : 3.56 % Allowed : 22.57 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.16 (0.17), residues: 2325 helix: 0.58 (0.15), residues: 1119 sheet: -2.35 (0.31), residues: 245 loop : -1.95 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B1104 HIS 0.005 0.001 HIS B 890 PHE 0.019 0.001 PHE B 624 TYR 0.014 0.001 TYR B 559 ARG 0.004 0.000 ARG B 620 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 866) hydrogen bonds : angle 4.93040 ( 2469) covalent geometry : bond 0.00277 (19857) covalent geometry : angle 0.59481 (26930) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 198 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 GLN cc_start: 0.6993 (pm20) cc_final: 0.6771 (mp10) REVERT: A 940 GLN cc_start: 0.6829 (mm-40) cc_final: 0.6511 (mm-40) REVERT: A 986 GLN cc_start: 0.7682 (tm-30) cc_final: 0.7299 (tm-30) REVERT: A 989 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8077 (mm) REVERT: A 1028 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.4698 (t80) REVERT: A 1033 PHE cc_start: 0.8021 (m-80) cc_final: 0.7753 (m-80) REVERT: A 1130 LYS cc_start: 0.6519 (mttp) cc_final: 0.5232 (tppt) REVERT: B 50 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6716 (mt0) REVERT: B 238 HIS cc_start: 0.6923 (OUTLIER) cc_final: 0.6260 (m-70) REVERT: B 580 ASN cc_start: 0.7143 (t0) cc_final: 0.6860 (t0) REVERT: B 602 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.7189 (m-40) REVERT: B 641 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7271 (ttm170) REVERT: B 890 HIS cc_start: 0.8419 (OUTLIER) cc_final: 0.7168 (m-70) REVERT: B 978 MET cc_start: 0.6684 (OUTLIER) cc_final: 0.6270 (ptp) REVERT: B 1130 LYS cc_start: 0.7230 (mttp) cc_final: 0.6730 (mmtm) REVERT: B 1146 TYR cc_start: 0.6620 (m-80) cc_final: 0.6389 (m-80) outliers start: 74 outliers final: 38 residues processed: 249 average time/residue: 0.3112 time to fit residues: 118.1510 Evaluate side-chains 220 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1028 PHE Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1104 TRP Chi-restraints excluded: chain B residue 1134 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 118 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN A 441 ASN A 851 GLN B 486 ASN ** B 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN B 890 HIS B1042 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.177439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.141091 restraints weight = 27756.976| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 3.38 r_work: 0.3532 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 19857 Z= 0.307 Angle : 0.713 10.761 26930 Z= 0.365 Chirality : 0.046 0.225 2966 Planarity : 0.005 0.054 3415 Dihedral : 12.949 178.236 2800 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.39 % Favored : 91.40 % Rotamer: Outliers : 5.00 % Allowed : 21.85 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.38 (0.17), residues: 2325 helix: 0.38 (0.15), residues: 1127 sheet: -2.50 (0.30), residues: 259 loop : -2.01 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B1104 HIS 0.011 0.002 HIS A 238 PHE 0.015 0.002 PHE B 998 TYR 0.016 0.002 TYR B 559 ARG 0.005 0.001 ARG A 972 Details of bonding type rmsd hydrogen bonds : bond 0.05195 ( 866) hydrogen bonds : angle 5.07678 ( 2469) covalent geometry : bond 0.00720 (19857) covalent geometry : angle 0.71274 (26930) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 171 time to evaluate : 2.293 Fit side-chains revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7021 (tm-30) REVERT: A 463 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7268 (pm20) REVERT: A 940 GLN cc_start: 0.6840 (mm-40) cc_final: 0.6456 (mm-40) REVERT: A 986 GLN cc_start: 0.7753 (tm-30) cc_final: 0.7334 (tm-30) REVERT: A 989 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8034 (mm) REVERT: A 1028 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.4942 (t80) REVERT: A 1030 ARG cc_start: 0.7586 (ptt90) cc_final: 0.7315 (ppt90) REVERT: A 1130 LYS cc_start: 0.6545 (mttp) cc_final: 0.5224 (tppt) REVERT: B 50 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6682 (mt0) REVERT: B 93 ASP cc_start: 0.7786 (t0) cc_final: 0.7582 (t0) REVERT: B 238 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.6747 (m-70) REVERT: B 580 ASN cc_start: 0.7241 (t0) cc_final: 0.7031 (t0) REVERT: B 602 ASN cc_start: 0.7472 (OUTLIER) cc_final: 0.7211 (m-40) REVERT: B 641 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7370 (ttm170) REVERT: B 881 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7627 (tp30) REVERT: B 978 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6629 (ptp) REVERT: B 1082 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.4404 (mm-30) REVERT: B 1130 LYS cc_start: 0.7197 (mttp) cc_final: 0.6912 (tptt) outliers start: 104 outliers final: 65 residues processed: 253 average time/residue: 0.3028 time to fit residues: 119.8341 Evaluate side-chains 233 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 157 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1028 PHE Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1103 TYR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 793 ASN Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 992 ASP Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1082 GLU Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain B residue 1104 TRP Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1134 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 143 optimal weight: 0.7980 chunk 137 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN A 851 GLN B 453 GLN ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.181179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.144985 restraints weight = 27672.250| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 3.13 r_work: 0.3606 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19857 Z= 0.144 Angle : 0.597 9.309 26930 Z= 0.306 Chirality : 0.040 0.192 2966 Planarity : 0.004 0.047 3415 Dihedral : 12.633 179.178 2800 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.10 % Favored : 92.69 % Rotamer: Outliers : 4.19 % Allowed : 22.86 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.01 (0.17), residues: 2325 helix: 0.74 (0.16), residues: 1132 sheet: -2.25 (0.32), residues: 238 loop : -1.98 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B1104 HIS 0.004 0.001 HIS B 134 PHE 0.020 0.001 PHE A1033 TYR 0.014 0.001 TYR B 559 ARG 0.004 0.000 ARG A 954 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 866) hydrogen bonds : angle 4.69365 ( 2469) covalent geometry : bond 0.00329 (19857) covalent geometry : angle 0.59670 (26930) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 193 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: A 463 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7056 (pm20) REVERT: A 508 GLN cc_start: 0.7136 (pm20) cc_final: 0.6879 (mp10) REVERT: A 691 LYS cc_start: 0.7114 (pttm) cc_final: 0.6631 (mmtt) REVERT: A 908 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6559 (tt0) REVERT: A 940 GLN cc_start: 0.6972 (mm-40) cc_final: 0.6587 (mm-40) REVERT: A 989 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8065 (mm) REVERT: A 1028 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.4858 (t80) REVERT: A 1130 LYS cc_start: 0.6500 (mttp) cc_final: 0.5282 (tppt) REVERT: A 1186 TRP cc_start: 0.6214 (t60) cc_final: 0.5691 (t-100) REVERT: B 50 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6787 (mt0) REVERT: B 93 ASP cc_start: 0.7660 (t0) cc_final: 0.7437 (t0) REVERT: B 238 HIS cc_start: 0.6989 (OUTLIER) cc_final: 0.6259 (m-70) REVERT: B 580 ASN cc_start: 0.7174 (t0) cc_final: 0.6913 (t0) REVERT: B 602 ASN cc_start: 0.7538 (OUTLIER) cc_final: 0.7291 (m-40) REVERT: B 641 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7318 (ttm170) REVERT: B 881 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7480 (tp30) REVERT: B 978 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.6400 (ptp) outliers start: 87 outliers final: 52 residues processed: 260 average time/residue: 0.3222 time to fit residues: 128.0300 Evaluate side-chains 247 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 184 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1028 PHE Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1103 TYR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 793 ASN Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain B residue 1104 TRP Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1134 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 194 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 232 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN A 851 GLN ** B 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.178701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.142417 restraints weight = 27308.974| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 3.10 r_work: 0.3540 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19857 Z= 0.209 Angle : 0.634 10.764 26930 Z= 0.323 Chirality : 0.042 0.242 2966 Planarity : 0.004 0.081 3415 Dihedral : 12.503 179.755 2800 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.17 % Favored : 91.70 % Rotamer: Outliers : 4.52 % Allowed : 23.05 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.04 (0.17), residues: 2325 helix: 0.69 (0.15), residues: 1138 sheet: -2.24 (0.32), residues: 238 loop : -1.98 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B1104 HIS 0.007 0.001 HIS A 238 PHE 0.018 0.002 PHE A1131 TYR 0.015 0.002 TYR B 315 ARG 0.007 0.000 ARG A1001 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 866) hydrogen bonds : angle 4.72610 ( 2469) covalent geometry : bond 0.00488 (19857) covalent geometry : angle 0.63393 (26930) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 190 time to evaluate : 1.950 Fit side-chains revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7009 (tm-30) REVERT: A 463 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7158 (pm20) REVERT: A 691 LYS cc_start: 0.7042 (pttm) cc_final: 0.6589 (mmtt) REVERT: A 908 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6440 (tt0) REVERT: A 940 GLN cc_start: 0.6915 (mm-40) cc_final: 0.6531 (mm-40) REVERT: A 989 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8114 (mm) REVERT: A 1028 PHE cc_start: 0.6874 (OUTLIER) cc_final: 0.4892 (t80) REVERT: A 1130 LYS cc_start: 0.6503 (mttp) cc_final: 0.5117 (tppt) REVERT: B 50 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6667 (mt0) REVERT: B 238 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.6592 (m-70) REVERT: B 576 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7512 (mtmm) REVERT: B 580 ASN cc_start: 0.7203 (t0) cc_final: 0.6972 (t0) REVERT: B 602 ASN cc_start: 0.7509 (OUTLIER) cc_final: 0.7264 (m-40) REVERT: B 641 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7330 (ttm170) REVERT: B 881 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7577 (tp30) REVERT: B 978 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6548 (ptp) REVERT: B 1031 LYS cc_start: 0.7671 (mttt) cc_final: 0.7402 (mtmt) REVERT: B 1082 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.4274 (mm-30) REVERT: B 1130 LYS cc_start: 0.6032 (tptt) cc_final: 0.5559 (tptt) REVERT: B 1186 TRP cc_start: 0.7002 (t-100) cc_final: 0.6711 (t-100) outliers start: 94 outliers final: 64 residues processed: 262 average time/residue: 0.3178 time to fit residues: 127.7695 Evaluate side-chains 248 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 172 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1028 PHE Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1103 TYR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 793 ASN Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1082 GLU Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain B residue 1104 TRP Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1134 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 203 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 159 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS A 181 ASN A 307 HIS A 851 GLN ** B 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.178780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.142575 restraints weight = 27100.472| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 3.13 r_work: 0.3533 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19857 Z= 0.207 Angle : 0.632 9.760 26930 Z= 0.322 Chirality : 0.042 0.229 2966 Planarity : 0.004 0.068 3415 Dihedral : 12.333 179.773 2800 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.91 % Favored : 91.96 % Rotamer: Outliers : 4.91 % Allowed : 23.15 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.00 (0.17), residues: 2325 helix: 0.73 (0.15), residues: 1129 sheet: -2.19 (0.32), residues: 238 loop : -1.96 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B1104 HIS 0.006 0.001 HIS A 238 PHE 0.014 0.002 PHE A1033 TYR 0.014 0.002 TYR B 559 ARG 0.006 0.000 ARG B1030 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 866) hydrogen bonds : angle 4.69199 ( 2469) covalent geometry : bond 0.00484 (19857) covalent geometry : angle 0.63240 (26930) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 185 time to evaluate : 2.117 Fit side-chains revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: A 463 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7122 (pm20) REVERT: A 908 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6343 (tt0) REVERT: A 940 GLN cc_start: 0.6945 (mm-40) cc_final: 0.6593 (mm-40) REVERT: A 989 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8052 (mm) REVERT: A 1004 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: A 1130 LYS cc_start: 0.6512 (mttp) cc_final: 0.5214 (tppt) REVERT: A 1186 TRP cc_start: 0.6134 (t60) cc_final: 0.5605 (t-100) REVERT: B 50 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6671 (mt0) REVERT: B 74 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7656 (mt-10) REVERT: B 238 HIS cc_start: 0.7241 (OUTLIER) cc_final: 0.6507 (m-70) REVERT: B 576 LYS cc_start: 0.7775 (mtpt) cc_final: 0.7543 (mtmm) REVERT: B 580 ASN cc_start: 0.7211 (t0) cc_final: 0.6929 (t0) REVERT: B 602 ASN cc_start: 0.7518 (OUTLIER) cc_final: 0.7283 (m-40) REVERT: B 641 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7313 (ttm170) REVERT: B 881 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7549 (tp30) REVERT: B 978 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6406 (ptp) REVERT: B 1031 LYS cc_start: 0.7683 (mttt) cc_final: 0.7406 (mtmt) REVERT: B 1082 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.4249 (mm-30) REVERT: B 1130 LYS cc_start: 0.6013 (tptt) cc_final: 0.5434 (tptt) REVERT: B 1186 TRP cc_start: 0.6864 (t-100) cc_final: 0.6532 (t-100) outliers start: 102 outliers final: 74 residues processed: 263 average time/residue: 0.3065 time to fit residues: 124.4361 Evaluate side-chains 262 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 175 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 781 GLN Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1004 TYR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1103 TYR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 793 ASN Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 992 ASP Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1063 GLU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1082 GLU Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain B residue 1104 TRP Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1134 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 44 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 162 optimal weight: 0.5980 chunk 232 optimal weight: 20.0000 chunk 221 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 chunk 185 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.184492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.148294 restraints weight = 27479.199| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 3.03 r_work: 0.3632 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19857 Z= 0.120 Angle : 0.577 9.482 26930 Z= 0.295 Chirality : 0.039 0.213 2966 Planarity : 0.003 0.043 3415 Dihedral : 11.985 178.001 2800 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.75 % Favored : 93.12 % Rotamer: Outliers : 3.27 % Allowed : 24.78 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.66 (0.18), residues: 2325 helix: 1.02 (0.16), residues: 1133 sheet: -2.06 (0.32), residues: 242 loop : -1.81 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B1098 HIS 0.005 0.001 HIS B 623 PHE 0.012 0.001 PHE B 448 TYR 0.014 0.001 TYR B 559 ARG 0.005 0.000 ARG B 936 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 866) hydrogen bonds : angle 4.46997 ( 2469) covalent geometry : bond 0.00267 (19857) covalent geometry : angle 0.57701 (26930) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 203 time to evaluate : 2.191 Fit side-chains revert: symmetry clash REVERT: A 13 PHE cc_start: 0.8430 (m-80) cc_final: 0.8119 (m-80) REVERT: A 112 GLN cc_start: 0.6557 (tp40) cc_final: 0.6212 (tp40) REVERT: A 207 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: A 463 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: A 508 GLN cc_start: 0.7103 (pm20) cc_final: 0.6902 (mp10) REVERT: A 580 ASN cc_start: 0.7237 (t0) cc_final: 0.6899 (t0) REVERT: A 691 LYS cc_start: 0.6840 (pttm) cc_final: 0.6437 (mmtt) REVERT: A 908 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6399 (tt0) REVERT: A 940 GLN cc_start: 0.6995 (mm-40) cc_final: 0.6661 (mm-40) REVERT: A 1130 LYS cc_start: 0.6314 (mttp) cc_final: 0.5049 (tptt) REVERT: A 1186 TRP cc_start: 0.6250 (t60) cc_final: 0.5758 (t-100) REVERT: B 50 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6578 (mt0) REVERT: B 238 HIS cc_start: 0.6843 (OUTLIER) cc_final: 0.6139 (m-70) REVERT: B 315 TYR cc_start: 0.8195 (m-80) cc_final: 0.7892 (m-80) REVERT: B 580 ASN cc_start: 0.7172 (t0) cc_final: 0.6875 (t0) REVERT: B 602 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.7222 (m-40) REVERT: B 641 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7273 (ttm170) REVERT: B 881 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7422 (tp30) REVERT: B 978 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.6157 (ptp) REVERT: B 1130 LYS cc_start: 0.5859 (tptt) cc_final: 0.5206 (tptt) REVERT: B 1186 TRP cc_start: 0.6735 (t-100) cc_final: 0.6375 (t-100) outliers start: 68 outliers final: 46 residues processed: 249 average time/residue: 0.3144 time to fit residues: 121.4168 Evaluate side-chains 235 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 180 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1103 TYR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 793 ASN Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1063 GLU Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain B residue 1104 TRP Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1134 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 186 optimal weight: 20.0000 chunk 181 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN A 851 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.179703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.142998 restraints weight = 27229.278| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.96 r_work: 0.3564 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19857 Z= 0.193 Angle : 0.633 11.266 26930 Z= 0.321 Chirality : 0.042 0.236 2966 Planarity : 0.004 0.052 3415 Dihedral : 11.858 179.362 2800 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.78 % Favored : 92.09 % Rotamer: Outliers : 3.80 % Allowed : 24.40 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.67 (0.18), residues: 2325 helix: 1.02 (0.16), residues: 1125 sheet: -2.09 (0.33), residues: 242 loop : -1.79 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B1104 HIS 0.011 0.001 HIS B 553 PHE 0.012 0.001 PHE A1033 TYR 0.014 0.001 TYR B 559 ARG 0.004 0.000 ARG B 936 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 866) hydrogen bonds : angle 4.55467 ( 2469) covalent geometry : bond 0.00450 (19857) covalent geometry : angle 0.63254 (26930) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 181 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.6571 (tp40) cc_final: 0.6193 (tp40) REVERT: A 207 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: A 463 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7058 (pm20) REVERT: A 508 GLN cc_start: 0.7143 (pm20) cc_final: 0.6931 (mp10) REVERT: A 580 ASN cc_start: 0.7130 (t0) cc_final: 0.6846 (t0) REVERT: A 691 LYS cc_start: 0.6945 (pttm) cc_final: 0.6528 (mmtt) REVERT: A 908 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6395 (tt0) REVERT: A 940 GLN cc_start: 0.7060 (mm-40) cc_final: 0.6653 (mm-40) REVERT: A 1130 LYS cc_start: 0.6291 (mttp) cc_final: 0.5022 (tptt) REVERT: A 1186 TRP cc_start: 0.6227 (t60) cc_final: 0.5617 (t-100) REVERT: B 238 HIS cc_start: 0.7088 (OUTLIER) cc_final: 0.6277 (m-70) REVERT: B 580 ASN cc_start: 0.7185 (t0) cc_final: 0.6922 (t0) REVERT: B 602 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7266 (m-40) REVERT: B 641 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7320 (ttm170) REVERT: B 881 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7462 (tp30) REVERT: B 978 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6293 (ptp) REVERT: B 1082 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.4091 (mm-30) REVERT: B 1130 LYS cc_start: 0.5929 (tptt) cc_final: 0.5287 (tptt) REVERT: B 1186 TRP cc_start: 0.6737 (t-100) cc_final: 0.6421 (t-100) outliers start: 79 outliers final: 60 residues processed: 243 average time/residue: 0.3047 time to fit residues: 115.8834 Evaluate side-chains 245 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 176 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1103 TYR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 793 ASN Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1082 GLU Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain B residue 1104 TRP Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1134 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 157 optimal weight: 0.7980 chunk 221 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 112 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.184389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.147040 restraints weight = 27377.269| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.97 r_work: 0.3633 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19857 Z= 0.131 Angle : 0.600 12.380 26930 Z= 0.304 Chirality : 0.040 0.217 2966 Planarity : 0.004 0.042 3415 Dihedral : 11.689 177.909 2800 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.01 % Favored : 92.86 % Rotamer: Outliers : 3.37 % Allowed : 24.74 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.56 (0.18), residues: 2325 helix: 1.10 (0.16), residues: 1139 sheet: -2.01 (0.33), residues: 242 loop : -1.76 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B1098 HIS 0.008 0.001 HIS B 553 PHE 0.012 0.001 PHE B 448 TYR 0.013 0.001 TYR B 559 ARG 0.005 0.000 ARG B1030 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 866) hydrogen bonds : angle 4.44006 ( 2469) covalent geometry : bond 0.00298 (19857) covalent geometry : angle 0.60021 (26930) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 192 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8230 (t70) cc_final: 0.7994 (t0) REVERT: A 112 GLN cc_start: 0.6627 (tp40) cc_final: 0.6277 (tp40) REVERT: A 207 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: A 463 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: A 508 GLN cc_start: 0.7104 (pm20) cc_final: 0.6903 (mp10) REVERT: A 580 ASN cc_start: 0.7163 (t0) cc_final: 0.6818 (t0) REVERT: A 691 LYS cc_start: 0.6974 (pttm) cc_final: 0.6529 (mmtt) REVERT: A 908 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6273 (tt0) REVERT: A 940 GLN cc_start: 0.7049 (mm-40) cc_final: 0.6612 (mm-40) REVERT: A 1130 LYS cc_start: 0.6331 (mttp) cc_final: 0.5103 (tptt) REVERT: A 1186 TRP cc_start: 0.6188 (t60) cc_final: 0.5621 (t-100) REVERT: B 238 HIS cc_start: 0.6809 (OUTLIER) cc_final: 0.6011 (m-70) REVERT: B 580 ASN cc_start: 0.7169 (t0) cc_final: 0.6932 (t0) REVERT: B 602 ASN cc_start: 0.7526 (OUTLIER) cc_final: 0.7277 (m-40) REVERT: B 641 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7319 (ttm170) REVERT: B 881 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7435 (tp30) REVERT: B 978 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.6117 (ptp) REVERT: B 1082 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.4017 (mm-30) REVERT: B 1130 LYS cc_start: 0.5903 (tptt) cc_final: 0.5265 (tptt) REVERT: B 1186 TRP cc_start: 0.6668 (t-100) cc_final: 0.6290 (t-100) outliers start: 70 outliers final: 51 residues processed: 242 average time/residue: 0.3213 time to fit residues: 119.9512 Evaluate side-chains 245 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1103 TYR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 793 ASN Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1082 GLU Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain B residue 1104 TRP Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1134 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 111 optimal weight: 6.9990 chunk 225 optimal weight: 0.0370 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN A 851 GLN B 833 GLN 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 = 0.182823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.146303 restraints weight = 27138.612| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.92 r_work: 0.3620 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19857 Z= 0.150 Angle : 0.611 11.706 26930 Z= 0.309 Chirality : 0.040 0.212 2966 Planarity : 0.004 0.041 3415 Dihedral : 11.603 178.432 2800 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.35 % Favored : 92.52 % Rotamer: Outliers : 3.56 % Allowed : 24.59 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.18), residues: 2325 helix: 1.12 (0.16), residues: 1139 sheet: -1.99 (0.33), residues: 242 loop : -1.74 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B1104 HIS 0.009 0.001 HIS B 553 PHE 0.013 0.001 PHE B1033 TYR 0.014 0.001 TYR B 315 ARG 0.005 0.000 ARG B1030 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 866) hydrogen bonds : angle 4.45503 ( 2469) covalent geometry : bond 0.00347 (19857) covalent geometry : angle 0.61111 (26930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9027.07 seconds wall clock time: 157 minutes 32.93 seconds (9452.93 seconds total)