Starting phenix.real_space_refine on Tue Jun 17 04:04:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9khz_62360/06_2025/9khz_62360.cif Found real_map, /net/cci-nas-00/data/ceres_data/9khz_62360/06_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_62360/06_2025/9khz_62360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9khz_62360/06_2025/9khz_62360.map" model { file = "/net/cci-nas-00/data/ceres_data/9khz_62360/06_2025/9khz_62360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9khz_62360/06_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-5710/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: 14.37, per 1000 atoms: 0.74 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: 5.11 Conformation dependent library (CDL) restraints added in 2.6 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: 2.96 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: 8.73 Time building geometry restraints manager: 6.12 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: 2.060 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: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 51.640 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.910 ------------------------------------------------------------------------------- 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 : 1.963 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: 0.3466 time to fit residues: 101.0030 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 : 2.291 ------------------------------------------------------------------------------- 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 = 0.176109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.139517 restraints weight = 27835.278| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 3.44 r_work: 0.3473 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 0.079 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 : 2.212 Fit side-chains revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.6981 (tm-30) REVERT: A 809 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: A 940 GLN cc_start: 0.6856 (mm-40) cc_final: 0.6544 (mm-40) REVERT: A 1028 PHE cc_start: 0.6880 (OUTLIER) cc_final: 0.4707 (t80) REVERT: A 1130 LYS cc_start: 0.6556 (mttp) cc_final: 0.5241 (tppt) REVERT: B 205 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7755 (mttp) REVERT: B 238 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.6875 (m-70) REVERT: B 858 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7041 (mtt-85) REVERT: B 890 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.6708 (m90) REVERT: B 978 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6542 (ptp) outliers start: 117 outliers final: 58 residues processed: 274 average time/residue: 0.3476 time to fit residues: 145.9559 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 : 2.275 ------------------------------------------------------------------------------- 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: 0.9990 chunk 119 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 168 optimal weight: 0.7980 chunk 8 optimal weight: 0.0970 chunk 159 optimal weight: 0.0980 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: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 A 577 GLN A 581 ASN A 668 ASN A 851 GLN A 951 GLN A 966 GLN A1042 ASN B 577 GLN B 581 ASN ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 HIS B 721 ASN B 890 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.183160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.147187 restraints weight = 27310.543| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.08 r_work: 0.3639 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1791 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= 0.124 Angle : 0.585 9.378 26930 Z= 0.305 Chirality : 0.040 0.160 2966 Planarity : 0.004 0.052 3415 Dihedral : 12.886 177.417 2804 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.88 % Favored : 92.95 % Rotamer: Outliers : 3.08 % Allowed : 23.05 % 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: -1.07 (0.17), residues: 2325 helix: 0.66 (0.16), residues: 1113 sheet: -2.33 (0.31), residues: 245 loop : -1.89 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B1104 HIS 0.030 0.001 HIS B 890 PHE 0.015 0.001 PHE A 448 TYR 0.014 0.001 TYR B 559 ARG 0.004 0.000 ARG A 959 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 866) hydrogen bonds : angle 4.86024 ( 2469) covalent geometry : bond 0.00263 (19857) covalent geometry : angle 0.58505 (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 270 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 206 time to evaluate : 2.163 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8153 (mtt) cc_final: 0.7755 (mtp) REVERT: A 508 GLN cc_start: 0.6965 (pm20) cc_final: 0.6758 (mp10) REVERT: A 940 GLN cc_start: 0.6898 (mm-40) cc_final: 0.6618 (mm-40) REVERT: A 986 GLN cc_start: 0.7661 (tm-30) cc_final: 0.7285 (tm-30) REVERT: A 989 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8098 (mm) REVERT: A 1028 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.4687 (t80) REVERT: A 1030 ARG cc_start: 0.7518 (ptt90) cc_final: 0.7306 (ppt90) REVERT: A 1130 LYS cc_start: 0.6510 (mttp) cc_final: 0.5230 (tppt) REVERT: B 50 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6718 (mt0) REVERT: B 104 ASP cc_start: 0.8472 (t70) cc_final: 0.8200 (t0) REVERT: B 238 HIS cc_start: 0.6816 (OUTLIER) cc_final: 0.6177 (m-70) REVERT: B 580 ASN cc_start: 0.7130 (t0) cc_final: 0.6855 (t0) REVERT: B 602 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.7174 (m-40) REVERT: B 641 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7248 (ttm170) REVERT: B 978 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.6234 (ptp) REVERT: B 1084 PHE cc_start: 0.7268 (m-80) cc_final: 0.6291 (m-80) REVERT: B 1130 LYS cc_start: 0.7185 (mttp) cc_final: 0.6836 (tptt) outliers start: 64 outliers final: 30 residues processed: 249 average time/residue: 0.3293 time to fit residues: 124.5176 Evaluate side-chains 213 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 671 LEU Chi-restraints excluded: chain A residue 724 LEU 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 122 LEU Chi-restraints excluded: chain B residue 135 LEU 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 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: 0.0370 chunk 198 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- 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 781 GLN A 851 GLN B 124 GLN B 486 ASN ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN B1042 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.178353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.142168 restraints weight = 27264.027| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 3.26 r_work: 0.3567 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19857 Z= 0.228 Angle : 0.644 10.214 26930 Z= 0.330 Chirality : 0.043 0.204 2966 Planarity : 0.004 0.050 3415 Dihedral : 12.753 179.929 2800 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.96 % Favored : 91.87 % Rotamer: Outliers : 4.38 % Allowed : 22.38 % Favored : 73.24 % 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: -1.13 (0.17), residues: 2325 helix: 0.59 (0.15), residues: 1133 sheet: -2.24 (0.32), residues: 236 loop : -1.99 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B1104 HIS 0.008 0.001 HIS A 238 PHE 0.025 0.002 PHE A1033 TYR 0.013 0.002 TYR B 559 ARG 0.005 0.000 ARG A 972 Details of bonding type rmsd hydrogen bonds : bond 0.04589 ( 866) hydrogen bonds : angle 4.86614 ( 2469) covalent geometry : bond 0.00534 (19857) covalent geometry : angle 0.64376 (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 282 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 191 time to evaluate : 2.177 Fit side-chains revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: A 940 GLN cc_start: 0.6882 (mm-40) cc_final: 0.6493 (mm-40) REVERT: A 986 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7341 (tm-30) REVERT: A 989 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8080 (mm) REVERT: A 1028 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.4805 (t80) REVERT: A 1030 ARG cc_start: 0.7556 (ptt90) cc_final: 0.7325 (ppt90) REVERT: A 1130 LYS cc_start: 0.6500 (mttp) cc_final: 0.5213 (tppt) REVERT: B 93 ASP cc_start: 0.7694 (t0) cc_final: 0.7465 (t0) REVERT: B 238 HIS cc_start: 0.7197 (OUTLIER) cc_final: 0.6506 (m-70) REVERT: B 358 SER cc_start: 0.8915 (t) cc_final: 0.8543 (m) REVERT: B 580 ASN cc_start: 0.7210 (t0) cc_final: 0.6970 (t0) REVERT: B 602 ASN cc_start: 0.7496 (OUTLIER) cc_final: 0.7216 (m-40) REVERT: B 641 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7293 (ttm170) REVERT: B 881 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7566 (tp30) REVERT: B 978 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6402 (ptp) REVERT: B 1130 LYS cc_start: 0.7132 (mttp) cc_final: 0.6925 (tptt) outliers start: 91 outliers final: 57 residues processed: 258 average time/residue: 0.3368 time to fit residues: 135.4996 Evaluate side-chains 238 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 2.080 ------------------------------------------------------------------------------- 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 201 ASP Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 551 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 781 GLN Chi-restraints excluded: chain A residue 803 SER 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 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 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 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 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 803 SER 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 1024 VAL Chi-restraints excluded: chain B residue 1035 CYS Chi-restraints excluded: chain B residue 1076 VAL 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: 2.9990 chunk 137 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 173 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 781 GLN A 851 GLN ** B 660 ASN ** 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 = 0.4340 r_free = 0.4340 target = 0.181228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.145007 restraints weight = 27684.142| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 3.24 r_work: 0.3598 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19857 Z= 0.156 Angle : 0.595 9.333 26930 Z= 0.306 Chirality : 0.040 0.168 2966 Planarity : 0.004 0.068 3415 Dihedral : 12.546 179.122 2800 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.35 % Favored : 92.47 % Rotamer: Outliers : 3.95 % Allowed : 23.00 % Favored : 73.05 % 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: -0.91 (0.17), residues: 2325 helix: 0.81 (0.16), residues: 1127 sheet: -2.21 (0.32), residues: 238 loop : -1.90 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B1104 HIS 0.005 0.001 HIS B 134 PHE 0.022 0.001 PHE A1033 TYR 0.013 0.001 TYR B 559 ARG 0.006 0.000 ARG A1001 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 866) hydrogen bonds : angle 4.67580 ( 2469) covalent geometry : bond 0.00359 (19857) covalent geometry : angle 0.59455 (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 271 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 189 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 PHE cc_start: 0.8447 (m-80) cc_final: 0.8122 (m-80) REVERT: A 67 MET cc_start: 0.8102 (mtt) cc_final: 0.7802 (mtt) REVERT: A 207 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: A 508 GLN cc_start: 0.7113 (pm20) cc_final: 0.6861 (mp10) REVERT: A 580 ASN cc_start: 0.7189 (t0) cc_final: 0.6930 (t0) REVERT: A 691 LYS cc_start: 0.7068 (pttm) cc_final: 0.6586 (mmtt) REVERT: A 853 VAL cc_start: 0.7891 (OUTLIER) cc_final: 0.7667 (t) REVERT: A 908 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6517 (tt0) REVERT: A 940 GLN cc_start: 0.6886 (mm-40) cc_final: 0.6471 (mm-40) REVERT: A 989 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8063 (mm) REVERT: A 1028 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.4819 (t80) REVERT: A 1030 ARG cc_start: 0.7777 (ptt90) cc_final: 0.7573 (ppt90) REVERT: A 1130 LYS cc_start: 0.6501 (mttp) cc_final: 0.5276 (tppt) REVERT: A 1186 TRP cc_start: 0.6130 (t60) cc_final: 0.5637 (t-100) REVERT: B 93 ASP cc_start: 0.7673 (t0) cc_final: 0.7447 (t0) REVERT: B 238 HIS cc_start: 0.6944 (OUTLIER) cc_final: 0.6153 (m-70) REVERT: B 580 ASN cc_start: 0.7187 (t0) cc_final: 0.6915 (t0) REVERT: B 602 ASN cc_start: 0.7527 (OUTLIER) cc_final: 0.7278 (m-40) REVERT: B 641 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7307 (ttm170) REVERT: B 881 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7550 (tp30) REVERT: B 978 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6227 (ptp) REVERT: B 1130 LYS cc_start: 0.7121 (mttp) cc_final: 0.6892 (tptt) REVERT: B 1186 TRP cc_start: 0.6809 (t-100) cc_final: 0.6528 (t-100) outliers start: 82 outliers final: 57 residues processed: 252 average time/residue: 0.3169 time to fit residues: 122.8225 Evaluate side-chains 246 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 179 time to evaluate : 2.099 ------------------------------------------------------------------------------- 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 149 VAL Chi-restraints excluded: chain A residue 150 LEU 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 471 SER Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 477 LEU 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 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 781 GLN Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 853 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 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 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 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 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 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 912 VAL Chi-restraints excluded: chain B residue 918 LEU 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 1024 VAL Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain B residue 1104 TRP 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: 0.5980 chunk 126 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 224 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 232 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- 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 660 ASN ** 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 = 0.4309 r_free = 0.4309 target = 0.178136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.142118 restraints weight = 27331.014| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.45 r_work: 0.3547 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 19857 Z= 0.245 Angle : 0.657 11.217 26930 Z= 0.334 Chirality : 0.043 0.245 2966 Planarity : 0.004 0.063 3415 Dihedral : 12.511 179.303 2800 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.09 % Favored : 91.78 % Rotamer: Outliers : 4.81 % Allowed : 22.47 % Favored : 72.71 % 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: 0.70 (0.15), residues: 1126 sheet: -2.37 (0.31), residues: 245 loop : -1.92 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B1104 HIS 0.008 0.001 HIS A 238 PHE 0.020 0.002 PHE A1033 TYR 0.015 0.002 TYR B 315 ARG 0.005 0.000 ARG A 972 Details of bonding type rmsd hydrogen bonds : bond 0.04544 ( 866) hydrogen bonds : angle 4.79029 ( 2469) covalent geometry : bond 0.00573 (19857) covalent geometry : angle 0.65678 (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 287 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 187 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7046 (tm-30) REVERT: A 691 LYS cc_start: 0.7060 (pttm) cc_final: 0.6604 (mmtt) REVERT: A 908 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6520 (tt0) REVERT: A 940 GLN cc_start: 0.6858 (mm-40) cc_final: 0.6461 (mm-40) REVERT: A 989 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8085 (mm) REVERT: A 1028 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.4871 (t80) REVERT: A 1030 ARG cc_start: 0.7464 (ptt90) cc_final: 0.7204 (ppt90) REVERT: A 1130 LYS cc_start: 0.6496 (mttp) cc_final: 0.5289 (tppt) REVERT: A 1186 TRP cc_start: 0.6193 (t60) cc_final: 0.5718 (t-100) REVERT: B 238 HIS cc_start: 0.7265 (OUTLIER) cc_final: 0.6516 (m-70) REVERT: B 358 SER cc_start: 0.8972 (t) cc_final: 0.8607 (m) REVERT: B 602 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7285 (m-40) REVERT: B 641 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7353 (ttm170) REVERT: B 881 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7603 (tp30) REVERT: B 978 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.6422 (ptp) REVERT: B 1030 ARG cc_start: 0.7201 (mtm110) cc_final: 0.6860 (mtm110) REVERT: B 1082 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.4190 (mm-30) outliers start: 100 outliers final: 65 residues processed: 263 average time/residue: 0.3230 time to fit residues: 131.7051 Evaluate side-chains 251 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 176 time to evaluate : 2.134 ------------------------------------------------------------------------------- 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 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 215 LEU 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 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 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 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 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 562 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 203 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 163 optimal weight: 0.3980 chunk 159 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 197 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 307 HIS A 781 GLN A 851 GLN B 453 GLN ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.181573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.145205 restraints weight = 27333.059| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 3.19 r_work: 0.3606 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2314 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= 0.141 Angle : 0.589 9.404 26930 Z= 0.301 Chirality : 0.040 0.225 2966 Planarity : 0.004 0.043 3415 Dihedral : 12.280 178.747 2800 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.40 % Favored : 92.47 % Rotamer: Outliers : 3.95 % Allowed : 23.39 % Favored : 72.67 % 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: -0.80 (0.18), residues: 2325 helix: 0.91 (0.16), residues: 1133 sheet: -2.16 (0.32), residues: 238 loop : -1.87 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B1104 HIS 0.005 0.001 HIS B 134 PHE 0.025 0.001 PHE A1131 TYR 0.014 0.001 TYR B 559 ARG 0.005 0.000 ARG A 954 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 866) hydrogen bonds : angle 4.56872 ( 2469) covalent geometry : bond 0.00322 (19857) covalent geometry : angle 0.58865 (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 278 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 196 time to evaluate : 2.080 Fit side-chains revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: A 463 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7118 (pm20) REVERT: A 508 GLN cc_start: 0.7122 (pm20) cc_final: 0.6877 (mp10) REVERT: A 580 ASN cc_start: 0.7235 (t0) cc_final: 0.6912 (t0) REVERT: A 691 LYS cc_start: 0.7029 (pttm) cc_final: 0.6581 (mmtt) REVERT: A 908 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6378 (tt0) REVERT: A 940 GLN cc_start: 0.7001 (mm-40) cc_final: 0.6601 (mm-40) REVERT: A 989 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8093 (mm) REVERT: A 1186 TRP cc_start: 0.6273 (t60) cc_final: 0.5708 (t-100) REVERT: B 238 HIS cc_start: 0.6860 (OUTLIER) cc_final: 0.6047 (m-70) REVERT: B 576 LYS cc_start: 0.7762 (mtpt) cc_final: 0.7532 (mtmm) REVERT: B 602 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.7278 (m-40) REVERT: B 641 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7286 (ttm170) REVERT: B 978 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6318 (ptp) REVERT: B 1030 ARG cc_start: 0.7098 (mtm110) cc_final: 0.6720 (mtm110) REVERT: B 1082 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.4206 (mm-30) REVERT: B 1130 LYS cc_start: 0.5803 (tptt) cc_final: 0.5011 (mmtm) REVERT: B 1186 TRP cc_start: 0.6682 (t-100) cc_final: 0.6176 (t-100) outliers start: 82 outliers final: 59 residues processed: 257 average time/residue: 0.3123 time to fit residues: 124.8718 Evaluate side-chains 251 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 183 time to evaluate : 2.082 ------------------------------------------------------------------------------- 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 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 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 562 GLU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 671 LEU 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 948 GLN Chi-restraints excluded: chain A residue 989 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 3 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 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 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 838 THR Chi-restraints excluded: chain B residue 859 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 44 optimal weight: 0.6980 chunk 103 optimal weight: 0.1980 chunk 50 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 232 optimal weight: 20.0000 chunk 221 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 660 ASN ** 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 = 0.4370 r_free = 0.4370 target = 0.183559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.147237 restraints weight = 27420.107| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 3.02 r_work: 0.3612 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19857 Z= 0.148 Angle : 0.596 10.382 26930 Z= 0.305 Chirality : 0.041 0.250 2966 Planarity : 0.004 0.042 3415 Dihedral : 12.040 178.109 2800 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.31 % Favored : 92.56 % Rotamer: Outliers : 3.95 % Allowed : 23.53 % Favored : 72.52 % 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: 1.01 (0.16), residues: 1130 sheet: -2.09 (0.32), residues: 238 loop : -1.78 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1104 HIS 0.005 0.001 HIS B 134 PHE 0.024 0.001 PHE A1131 TYR 0.013 0.001 TYR B 559 ARG 0.005 0.000 ARG A 972 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 866) hydrogen bonds : angle 4.52480 ( 2469) covalent geometry : bond 0.00339 (19857) covalent geometry : angle 0.59642 (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: 82 poor density : 189 time to evaluate : 2.040 Fit side-chains revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8225 (t70) cc_final: 0.7993 (t0) REVERT: A 207 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7003 (tm-30) REVERT: A 463 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6996 (pm20) REVERT: A 508 GLN cc_start: 0.7174 (pm20) cc_final: 0.6955 (mp10) REVERT: A 580 ASN cc_start: 0.7229 (t0) cc_final: 0.6905 (t0) REVERT: A 691 LYS cc_start: 0.7049 (pttm) cc_final: 0.6576 (mmtt) REVERT: A 908 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6438 (tt0) REVERT: A 940 GLN cc_start: 0.7002 (mm-40) cc_final: 0.6612 (mm-40) REVERT: A 1186 TRP cc_start: 0.6261 (t60) cc_final: 0.5710 (t-100) REVERT: B 238 HIS cc_start: 0.6882 (OUTLIER) cc_final: 0.6063 (m-70) REVERT: B 576 LYS cc_start: 0.7784 (mtpt) cc_final: 0.7531 (mtmm) REVERT: B 602 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.7257 (m-40) REVERT: B 641 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7305 (ttm170) REVERT: B 881 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7499 (tp30) REVERT: B 978 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.6410 (ptp) REVERT: B 1082 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.4159 (mm-30) REVERT: B 1130 LYS cc_start: 0.5870 (tptt) cc_final: 0.4994 (mmtm) REVERT: B 1186 TRP cc_start: 0.6628 (t-100) cc_final: 0.6102 (t-100) outliers start: 82 outliers final: 64 residues processed: 252 average time/residue: 0.3116 time to fit residues: 122.1599 Evaluate side-chains 249 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 176 time to evaluate : 2.332 ------------------------------------------------------------------------------- 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 60 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 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 275 ASP 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 568 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 727 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 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 3 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 149 VAL 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 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 680 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 186 optimal weight: 9.9990 chunk 181 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 303 ASN A 851 GLN ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.185128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.148818 restraints weight = 27407.130| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.98 r_work: 0.3639 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2585 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= 0.122 Angle : 0.585 9.458 26930 Z= 0.299 Chirality : 0.040 0.217 2966 Planarity : 0.003 0.041 3415 Dihedral : 11.741 176.604 2800 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.18 % Favored : 92.69 % Rotamer: Outliers : 3.27 % Allowed : 24.45 % Favored : 72.28 % 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: -0.49 (0.18), residues: 2325 helix: 1.18 (0.16), residues: 1130 sheet: -2.07 (0.32), residues: 242 loop : -1.70 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B1098 HIS 0.004 0.001 HIS B 134 PHE 0.030 0.001 PHE A1131 TYR 0.013 0.001 TYR B 559 ARG 0.006 0.000 ARG A1030 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 866) hydrogen bonds : angle 4.40807 ( 2469) covalent geometry : bond 0.00273 (19857) covalent geometry : angle 0.58546 (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 267 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 199 time to evaluate : 2.167 Fit side-chains revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8231 (t70) cc_final: 0.7985 (t0) REVERT: A 112 GLN cc_start: 0.6550 (tp40) cc_final: 0.6197 (tp40) REVERT: A 207 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: A 463 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: A 580 ASN cc_start: 0.7207 (t0) cc_final: 0.6864 (t0) REVERT: A 691 LYS cc_start: 0.6949 (pttm) cc_final: 0.6522 (mmtt) REVERT: A 908 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6307 (tt0) REVERT: A 940 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6643 (mm-40) REVERT: A 999 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6923 (m-80) REVERT: A 1186 TRP cc_start: 0.6362 (t60) cc_final: 0.5716 (t-100) REVERT: B 238 HIS cc_start: 0.6875 (OUTLIER) cc_final: 0.6051 (m-70) REVERT: B 602 ASN cc_start: 0.7495 (OUTLIER) cc_final: 0.7237 (m-40) REVERT: B 641 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7302 (ttm170) REVERT: B 680 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: B 978 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6206 (ptp) REVERT: B 1130 LYS cc_start: 0.5900 (tptt) cc_final: 0.5035 (mmtm) REVERT: B 1186 TRP cc_start: 0.6561 (t-100) cc_final: 0.6055 (t-100) outliers start: 68 outliers final: 53 residues processed: 251 average time/residue: 0.3284 time to fit residues: 127.7267 Evaluate side-chains 245 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 183 time to evaluate : 2.161 ------------------------------------------------------------------------------- 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 60 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 275 ASP 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 568 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 727 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 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 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 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 641 ARG Chi-restraints excluded: chain B residue 680 ASP 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 859 THR Chi-restraints excluded: chain B residue 912 VAL 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 1076 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 157 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 106 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 486 ASN ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.183680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.147392 restraints weight = 27304.288| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 3.01 r_work: 0.3614 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19857 Z= 0.164 Angle : 0.626 13.408 26930 Z= 0.317 Chirality : 0.041 0.218 2966 Planarity : 0.004 0.040 3415 Dihedral : 11.658 177.456 2800 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.10 % Favored : 92.77 % Rotamer: Outliers : 3.37 % Allowed : 24.40 % Favored : 72.23 % 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: -0.53 (0.18), residues: 2325 helix: 1.09 (0.16), residues: 1136 sheet: -2.09 (0.32), residues: 242 loop : -1.67 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1104 HIS 0.008 0.001 HIS B 553 PHE 0.037 0.002 PHE A1084 TYR 0.013 0.001 TYR B 315 ARG 0.006 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 866) hydrogen bonds : angle 4.50788 ( 2469) covalent geometry : bond 0.00383 (19857) covalent geometry : angle 0.62569 (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 258 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 188 time to evaluate : 2.187 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.6559 (tp40) cc_final: 0.6186 (tp40) REVERT: A 207 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: A 463 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: A 580 ASN cc_start: 0.7150 (t0) cc_final: 0.6819 (t0) REVERT: A 691 LYS cc_start: 0.6900 (pttm) cc_final: 0.6516 (mmtt) REVERT: A 908 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6308 (tt0) REVERT: A 940 GLN cc_start: 0.6981 (mm-40) cc_final: 0.6586 (mm-40) REVERT: A 1168 ILE cc_start: 0.5267 (mt) cc_final: 0.4999 (mp) REVERT: A 1186 TRP cc_start: 0.6332 (t60) cc_final: 0.5724 (t-100) REVERT: B 238 HIS cc_start: 0.6929 (OUTLIER) cc_final: 0.6114 (m-70) REVERT: B 602 ASN cc_start: 0.7519 (OUTLIER) cc_final: 0.7269 (m-40) REVERT: B 641 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7334 (ttm170) REVERT: B 978 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6328 (ptp) REVERT: B 1030 ARG cc_start: 0.7173 (mtm110) cc_final: 0.6811 (mtm110) REVERT: B 1082 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.4092 (mm-30) REVERT: B 1130 LYS cc_start: 0.5907 (tptt) cc_final: 0.5008 (mmtm) REVERT: B 1186 TRP cc_start: 0.6570 (t-100) cc_final: 0.6096 (t-100) outliers start: 70 outliers final: 56 residues processed: 244 average time/residue: 0.3068 time to fit residues: 115.9172 Evaluate side-chains 245 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 181 time to evaluate : 1.968 ------------------------------------------------------------------------------- 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 60 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 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 671 LEU Chi-restraints excluded: chain A residue 727 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 999 PHE Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1103 TYR Chi-restraints excluded: chain A residue 1115 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 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 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 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 912 VAL 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 1076 VAL Chi-restraints excluded: chain B residue 1082 GLU 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: 1.9990 chunk 225 optimal weight: 0.0470 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 0.0030 chunk 160 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 232 optimal weight: 9.9990 overall best weight: 0.8092 ------------------------------------------------------------------------------- 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 660 ASN ** 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 = 0.4386 r_free = 0.4386 target = 0.185300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.149025 restraints weight = 27453.199| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.94 r_work: 0.3647 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2736 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= 0.121 Angle : 0.591 9.831 26930 Z= 0.301 Chirality : 0.040 0.192 2966 Planarity : 0.003 0.041 3415 Dihedral : 11.505 176.058 2800 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.97 % Favored : 92.90 % Rotamer: Outliers : 3.27 % Allowed : 24.30 % 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: -0.38 (0.18), residues: 2325 helix: 1.24 (0.16), residues: 1139 sheet: -2.00 (0.33), residues: 242 loop : -1.63 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1104 HIS 0.008 0.001 HIS B 553 PHE 0.021 0.001 PHE A1033 TYR 0.013 0.001 TYR B 559 ARG 0.005 0.000 ARG A1030 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 866) hydrogen bonds : angle 4.40051 ( 2469) covalent geometry : bond 0.00271 (19857) covalent geometry : angle 0.59143 (26930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8870.82 seconds wall clock time: 153 minutes 23.47 seconds (9203.47 seconds total)