Starting phenix.real_space_refine on Fri Jan 17 17:39:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6i_44260/01_2025/9b6i_44260_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6i_44260/01_2025/9b6i_44260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b6i_44260/01_2025/9b6i_44260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6i_44260/01_2025/9b6i_44260.map" model { file = "/net/cci-nas-00/data/ceres_data/9b6i_44260/01_2025/9b6i_44260_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6i_44260/01_2025/9b6i_44260_trim.cif" } resolution = 3.26 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= 0.044 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 S 136 5.16 5 C 18476 2.51 5 N 4556 2.21 5 O 5052 1.98 5 F 24 1.80 5 H 27072 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 55320 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 856, 13656 Classifications: {'peptide': 856} Link IDs: {'PTRANS': 19, 'TRANS': 836} Chain breaks: 10 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 174 Unusual residues: {' CA': 1, 'T14': 1, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Restraints were copied for chains: C, B, D Time building chain proxies: 37.64, per 1000 atoms: 0.68 Number of scatterers: 55320 At special positions: 0 Unit cell: (150.12, 150.12, 155.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 136 16.00 F 24 9.00 O 5052 8.00 N 4556 7.00 C 18476 6.00 H 27072 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 946 " distance=2.03 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: 12.44 Conformation dependent library (CDL) restraints added in 3.4 seconds 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6512 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 4 sheets defined 72.1% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 138 through 147 removed outlier: 3.724A pdb=" N LEU A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 186 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 286 through 298 Processing helix chain 'A' and resid 319 through 332 Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 361 through 372 Processing helix chain 'A' and resid 372 through 379 removed outlier: 3.856A pdb=" N ILE A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER A 377 " --> pdb=" O PRO A 373 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 397 removed outlier: 4.475A pdb=" N SER A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 448 through 456 removed outlier: 3.851A pdb=" N ALA A 452 " --> pdb=" O GLN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 479 removed outlier: 4.228A pdb=" N VAL A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 499 through 509 Processing helix chain 'A' and resid 512 through 526 Processing helix chain 'A' and resid 528 through 544 removed outlier: 4.053A pdb=" N GLY A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 581 Processing helix chain 'A' and resid 583 through 592 Processing helix chain 'A' and resid 596 through 614 removed outlier: 3.663A pdb=" N VAL A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 646 Processing helix chain 'A' and resid 646 through 656 removed outlier: 3.967A pdb=" N GLU A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN A 652 " --> pdb=" O ASP A 648 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 653 " --> pdb=" O LEU A 649 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 654 " --> pdb=" O ALA A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 673 Processing helix chain 'A' and resid 675 through 680 Processing helix chain 'A' and resid 681 through 694 Processing helix chain 'A' and resid 701 through 709 removed outlier: 3.739A pdb=" N ILE A 705 " --> pdb=" O LYS A 701 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 706 " --> pdb=" O ASN A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 742 removed outlier: 3.606A pdb=" N PHE A 740 " --> pdb=" O TYR A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 768 Processing helix chain 'A' and resid 775 through 796 removed outlier: 3.681A pdb=" N TYR A 794 " --> pdb=" O CYS A 790 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET A 795 " --> pdb=" O ASP A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 824 removed outlier: 3.637A pdb=" N VAL A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 853 removed outlier: 3.733A pdb=" N SER A 833 " --> pdb=" O SER A 829 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 843 " --> pdb=" O CYS A 839 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 844 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU A 849 " --> pdb=" O PHE A 845 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE A 850 " --> pdb=" O THR A 846 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N HIS A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 856 No H-bonds generated for 'chain 'A' and resid 854 through 856' Processing helix chain 'A' and resid 859 through 866 removed outlier: 3.596A pdb=" N LEU A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 896 Processing helix chain 'A' and resid 901 through 910 removed outlier: 3.510A pdb=" N PHE A 906 " --> pdb=" O TRP A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 removed outlier: 3.837A pdb=" N MET A 917 " --> pdb=" O PRO A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 975 removed outlier: 3.543A pdb=" N LEU A 965 " --> pdb=" O ILE A 961 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 992 Processing helix chain 'A' and resid 992 through 1011 removed outlier: 3.693A pdb=" N ASP A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 998 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A1005 " --> pdb=" O LYS A1001 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE A1006 " --> pdb=" O PHE A1002 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR A1011 " --> pdb=" O LEU A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1075 Processing helix chain 'A' and resid 1075 through 1081 removed outlier: 3.599A pdb=" N SER A1080 " --> pdb=" O LYS A1076 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1110 removed outlier: 4.066A pdb=" N GLN A1090 " --> pdb=" O HIS A1086 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A1091 " --> pdb=" O ARG A1087 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A1092 " --> pdb=" O PHE A1088 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA A1093 " --> pdb=" O ARG A1089 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS A1094 " --> pdb=" O GLN A1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 removed outlier: 3.724A pdb=" N LEU B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN B 145 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 186 Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'B' and resid 319 through 332 Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.857A pdb=" N ILE B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 377 " --> pdb=" O PRO B 373 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG B 378 " --> pdb=" O ARG B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 397 removed outlier: 4.474A pdb=" N SER B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 448 through 456 removed outlier: 3.851A pdb=" N ALA B 452 " --> pdb=" O GLN B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 479 removed outlier: 4.228A pdb=" N VAL B 471 " --> pdb=" O ASP B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 493 through 498 Processing helix chain 'B' and resid 499 through 509 Processing helix chain 'B' and resid 512 through 526 Processing helix chain 'B' and resid 528 through 544 removed outlier: 4.052A pdb=" N GLY B 544 " --> pdb=" O ASP B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 581 Processing helix chain 'B' and resid 583 through 592 Processing helix chain 'B' and resid 596 through 614 removed outlier: 3.662A pdb=" N VAL B 614 " --> pdb=" O SER B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 646 Processing helix chain 'B' and resid 646 through 656 removed outlier: 3.968A pdb=" N GLU B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN B 652 " --> pdb=" O ASP B 648 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 653 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 654 " --> pdb=" O ALA B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 673 Processing helix chain 'B' and resid 675 through 680 Processing helix chain 'B' and resid 681 through 694 Processing helix chain 'B' and resid 701 through 709 removed outlier: 3.738A pdb=" N ILE B 705 " --> pdb=" O LYS B 701 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 706 " --> pdb=" O ASN B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 742 removed outlier: 3.606A pdb=" N PHE B 740 " --> pdb=" O TYR B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 768 Processing helix chain 'B' and resid 775 through 796 removed outlier: 3.681A pdb=" N TYR B 794 " --> pdb=" O CYS B 790 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET B 795 " --> pdb=" O ASP B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 824 removed outlier: 3.638A pdb=" N VAL B 807 " --> pdb=" O ASP B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 853 removed outlier: 3.734A pdb=" N SER B 833 " --> pdb=" O SER B 829 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 843 " --> pdb=" O CYS B 839 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL B 844 " --> pdb=" O LEU B 840 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU B 849 " --> pdb=" O PHE B 845 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE B 850 " --> pdb=" O THR B 846 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N HIS B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 856 No H-bonds generated for 'chain 'B' and resid 854 through 856' Processing helix chain 'B' and resid 859 through 866 removed outlier: 3.596A pdb=" N LEU B 866 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 896 Processing helix chain 'B' and resid 901 through 910 removed outlier: 3.510A pdb=" N PHE B 906 " --> pdb=" O TRP B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 917 removed outlier: 3.836A pdb=" N MET B 917 " --> pdb=" O PRO B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 975 removed outlier: 3.544A pdb=" N LEU B 965 " --> pdb=" O ILE B 961 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 975 " --> pdb=" O LEU B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 992 Processing helix chain 'B' and resid 992 through 1011 removed outlier: 3.693A pdb=" N ASP B 997 " --> pdb=" O GLN B 993 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN B 998 " --> pdb=" O GLU B 994 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE B1005 " --> pdb=" O LYS B1001 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE B1006 " --> pdb=" O PHE B1002 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR B1011 " --> pdb=" O LEU B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1075 Processing helix chain 'B' and resid 1075 through 1081 removed outlier: 3.600A pdb=" N SER B1080 " --> pdb=" O LYS B1076 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER B1081 " --> pdb=" O ALA B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1110 removed outlier: 4.066A pdb=" N GLN B1090 " --> pdb=" O HIS B1086 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B1091 " --> pdb=" O ARG B1087 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP B1092 " --> pdb=" O PHE B1088 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA B1093 " --> pdb=" O ARG B1089 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS B1094 " --> pdb=" O GLN B1090 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 147 removed outlier: 3.724A pdb=" N LEU D 142 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN D 145 " --> pdb=" O ASP D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 186 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 286 through 298 Processing helix chain 'D' and resid 319 through 332 Processing helix chain 'D' and resid 345 through 353 Processing helix chain 'D' and resid 361 through 372 Processing helix chain 'D' and resid 372 through 379 removed outlier: 3.856A pdb=" N ILE D 376 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER D 377 " --> pdb=" O PRO D 373 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 397 removed outlier: 4.475A pdb=" N SER D 397 " --> pdb=" O GLU D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 428 Processing helix chain 'D' and resid 436 through 446 Processing helix chain 'D' and resid 448 through 456 removed outlier: 3.851A pdb=" N ALA D 452 " --> pdb=" O GLN D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 479 removed outlier: 4.227A pdb=" N VAL D 471 " --> pdb=" O ASP D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 490 Processing helix chain 'D' and resid 493 through 498 Processing helix chain 'D' and resid 499 through 509 Processing helix chain 'D' and resid 512 through 526 Processing helix chain 'D' and resid 528 through 544 removed outlier: 4.052A pdb=" N GLY D 544 " --> pdb=" O ASP D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 581 Processing helix chain 'D' and resid 583 through 592 Processing helix chain 'D' and resid 596 through 614 removed outlier: 3.662A pdb=" N VAL D 614 " --> pdb=" O SER D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 646 Processing helix chain 'D' and resid 646 through 656 removed outlier: 3.968A pdb=" N GLU D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN D 652 " --> pdb=" O ASP D 648 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D 653 " --> pdb=" O LEU D 649 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 654 " --> pdb=" O ALA D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 673 Processing helix chain 'D' and resid 675 through 680 Processing helix chain 'D' and resid 681 through 694 Processing helix chain 'D' and resid 701 through 709 removed outlier: 3.738A pdb=" N ILE D 705 " --> pdb=" O LYS D 701 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 706 " --> pdb=" O ASN D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 742 removed outlier: 3.606A pdb=" N PHE D 740 " --> pdb=" O TYR D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 768 Processing helix chain 'D' and resid 775 through 796 removed outlier: 3.681A pdb=" N TYR D 794 " --> pdb=" O CYS D 790 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET D 795 " --> pdb=" O ASP D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 824 removed outlier: 3.638A pdb=" N VAL D 807 " --> pdb=" O ASP D 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 853 removed outlier: 3.734A pdb=" N SER D 833 " --> pdb=" O SER D 829 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 843 " --> pdb=" O CYS D 839 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL D 844 " --> pdb=" O LEU D 840 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU D 849 " --> pdb=" O PHE D 845 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE D 850 " --> pdb=" O THR D 846 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N HIS D 851 " --> pdb=" O LEU D 847 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 856 No H-bonds generated for 'chain 'D' and resid 854 through 856' Processing helix chain 'D' and resid 859 through 866 removed outlier: 3.596A pdb=" N LEU D 866 " --> pdb=" O LYS D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 896 Processing helix chain 'D' and resid 901 through 910 removed outlier: 3.510A pdb=" N PHE D 906 " --> pdb=" O TRP D 902 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 917 removed outlier: 3.836A pdb=" N MET D 917 " --> pdb=" O PRO D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 975 removed outlier: 3.544A pdb=" N LEU D 965 " --> pdb=" O ILE D 961 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 975 " --> pdb=" O LEU D 971 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 992 Processing helix chain 'D' and resid 992 through 1011 removed outlier: 3.693A pdb=" N ASP D 997 " --> pdb=" O GLN D 993 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN D 998 " --> pdb=" O GLU D 994 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE D1005 " --> pdb=" O LYS D1001 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE D1006 " --> pdb=" O PHE D1002 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR D1011 " --> pdb=" O LEU D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1057 through 1075 Processing helix chain 'D' and resid 1075 through 1081 removed outlier: 3.600A pdb=" N SER D1080 " --> pdb=" O LYS D1076 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER D1081 " --> pdb=" O ALA D1077 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1110 removed outlier: 4.066A pdb=" N GLN D1090 " --> pdb=" O HIS D1086 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D1091 " --> pdb=" O ARG D1087 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP D1092 " --> pdb=" O PHE D1088 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA D1093 " --> pdb=" O ARG D1089 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS D1094 " --> pdb=" O GLN D1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 147 removed outlier: 3.724A pdb=" N LEU C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 186 Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 286 through 298 Processing helix chain 'C' and resid 319 through 332 Processing helix chain 'C' and resid 345 through 353 Processing helix chain 'C' and resid 361 through 372 Processing helix chain 'C' and resid 372 through 379 removed outlier: 3.856A pdb=" N ILE C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER C 377 " --> pdb=" O PRO C 373 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 378 " --> pdb=" O ARG C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 397 removed outlier: 4.475A pdb=" N SER C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 428 Processing helix chain 'C' and resid 436 through 446 Processing helix chain 'C' and resid 448 through 456 removed outlier: 3.851A pdb=" N ALA C 452 " --> pdb=" O GLN C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 479 removed outlier: 4.227A pdb=" N VAL C 471 " --> pdb=" O ASP C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'C' and resid 493 through 498 Processing helix chain 'C' and resid 499 through 509 Processing helix chain 'C' and resid 512 through 526 Processing helix chain 'C' and resid 528 through 544 removed outlier: 4.052A pdb=" N GLY C 544 " --> pdb=" O ASP C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 581 Processing helix chain 'C' and resid 583 through 592 Processing helix chain 'C' and resid 596 through 614 removed outlier: 3.663A pdb=" N VAL C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 646 Processing helix chain 'C' and resid 646 through 656 removed outlier: 3.967A pdb=" N GLU C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN C 652 " --> pdb=" O ASP C 648 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 654 " --> pdb=" O ALA C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 673 Processing helix chain 'C' and resid 675 through 680 Processing helix chain 'C' and resid 681 through 694 Processing helix chain 'C' and resid 701 through 709 removed outlier: 3.739A pdb=" N ILE C 705 " --> pdb=" O LYS C 701 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 706 " --> pdb=" O ASN C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 742 removed outlier: 3.606A pdb=" N PHE C 740 " --> pdb=" O TYR C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 768 Processing helix chain 'C' and resid 775 through 796 removed outlier: 3.681A pdb=" N TYR C 794 " --> pdb=" O CYS C 790 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET C 795 " --> pdb=" O ASP C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 824 removed outlier: 3.637A pdb=" N VAL C 807 " --> pdb=" O ASP C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 853 removed outlier: 3.732A pdb=" N SER C 833 " --> pdb=" O SER C 829 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C 843 " --> pdb=" O CYS C 839 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL C 844 " --> pdb=" O LEU C 840 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU C 849 " --> pdb=" O PHE C 845 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE C 850 " --> pdb=" O THR C 846 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N HIS C 851 " --> pdb=" O LEU C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 856 No H-bonds generated for 'chain 'C' and resid 854 through 856' Processing helix chain 'C' and resid 859 through 866 removed outlier: 3.596A pdb=" N LEU C 866 " --> pdb=" O LYS C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 896 Processing helix chain 'C' and resid 901 through 910 removed outlier: 3.511A pdb=" N PHE C 906 " --> pdb=" O TRP C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 917 removed outlier: 3.837A pdb=" N MET C 917 " --> pdb=" O PRO C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 975 removed outlier: 3.543A pdb=" N LEU C 965 " --> pdb=" O ILE C 961 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 992 Processing helix chain 'C' and resid 992 through 1011 removed outlier: 3.694A pdb=" N ASP C 997 " --> pdb=" O GLN C 993 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN C 998 " --> pdb=" O GLU C 994 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE C1005 " --> pdb=" O LYS C1001 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE C1006 " --> pdb=" O PHE C1002 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR C1011 " --> pdb=" O LEU C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1057 through 1075 Processing helix chain 'C' and resid 1075 through 1081 removed outlier: 3.600A pdb=" N SER C1080 " --> pdb=" O LYS C1076 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER C1081 " --> pdb=" O ALA C1077 " (cutoff:3.500A) Processing helix chain 'C' and resid 1084 through 1110 removed outlier: 4.066A pdb=" N GLN C1090 " --> pdb=" O HIS C1086 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C1091 " --> pdb=" O ARG C1087 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP C1092 " --> pdb=" O PHE C1088 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA C1093 " --> pdb=" O ARG C1089 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS C1094 " --> pdb=" O GLN C1090 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.811A pdb=" N HIS A 269 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 273 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL A 220 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP A 188 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU A 154 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE A 314 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE A 156 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 273 removed outlier: 3.810A pdb=" N HIS B 269 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 273 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL B 220 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP B 188 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 154 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE B 314 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 156 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 269 through 273 removed outlier: 3.811A pdb=" N HIS D 269 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 273 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL D 220 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP D 188 " --> pdb=" O ASN D 153 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU D 154 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE D 314 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE D 156 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.811A pdb=" N HIS C 269 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 273 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL C 220 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP C 188 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU C 154 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE C 314 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE C 156 " --> pdb=" O PHE C 314 " (cutoff:3.500A) 1676 hydrogen bonds defined for protein. 5016 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: 18.60 Time building geometry restraints manager: 14.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 27024 1.03 - 1.23: 106 1.23 - 1.42: 12202 1.42 - 1.62: 16448 1.62 - 1.81: 212 Bond restraints: 55992 Sorted by residual: bond pdb=" N20 T14 C1205 " pdb=" O21 T14 C1205 " ideal model delta sigma weight residual 1.347 1.207 0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" N20 T14 B1205 " pdb=" O21 T14 B1205 " ideal model delta sigma weight residual 1.347 1.207 0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" N20 T14 D1205 " pdb=" O21 T14 D1205 " ideal model delta sigma weight residual 1.347 1.207 0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" N20 T14 A1205 " pdb=" O21 T14 A1205 " ideal model delta sigma weight residual 1.347 1.208 0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C18 T14 C1205 " pdb=" C19 T14 C1205 " ideal model delta sigma weight residual 1.446 1.335 0.111 2.00e-02 2.50e+03 3.08e+01 ... (remaining 55987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 99999 2.58 - 5.16: 540 5.16 - 7.75: 109 7.75 - 10.33: 28 10.33 - 12.91: 24 Bond angle restraints: 100700 Sorted by residual: angle pdb=" CAT Y01 B1204 " pdb=" CBH Y01 B1204 " pdb=" CBF Y01 B1204 " ideal model delta sigma weight residual 108.46 95.55 12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" CAT Y01 D1204 " pdb=" CBH Y01 D1204 " pdb=" CBF Y01 D1204 " ideal model delta sigma weight residual 108.46 95.55 12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" CAT Y01 A1204 " pdb=" CBH Y01 A1204 " pdb=" CBF Y01 A1204 " ideal model delta sigma weight residual 108.46 95.56 12.90 3.00e+00 1.11e-01 1.85e+01 angle pdb=" CAT Y01 C1204 " pdb=" CBH Y01 C1204 " pdb=" CBF Y01 C1204 " ideal model delta sigma weight residual 108.46 95.56 12.90 3.00e+00 1.11e-01 1.85e+01 angle pdb=" CAT Y01 D1203 " pdb=" CBH Y01 D1203 " pdb=" CBF Y01 D1203 " ideal model delta sigma weight residual 108.46 95.57 12.89 3.00e+00 1.11e-01 1.85e+01 ... (remaining 100695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.91: 24384 14.91 - 29.82: 1830 29.82 - 44.73: 545 44.73 - 59.64: 312 59.64 - 74.55: 20 Dihedral angle restraints: 27091 sinusoidal: 14779 harmonic: 12312 Sorted by residual: dihedral pdb=" CA HIS D1086 " pdb=" C HIS D1086 " pdb=" N ARG D1087 " pdb=" CA ARG D1087 " ideal model delta harmonic sigma weight residual -180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA HIS A1086 " pdb=" C HIS A1086 " pdb=" N ARG A1087 " pdb=" CA ARG A1087 " ideal model delta harmonic sigma weight residual -180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA HIS B1086 " pdb=" C HIS B1086 " pdb=" N ARG B1087 " pdb=" CA ARG B1087 " ideal model delta harmonic sigma weight residual -180.00 -160.68 -19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 27088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4163 0.086 - 0.172: 177 0.172 - 0.258: 16 0.258 - 0.344: 32 0.344 - 0.431: 20 Chirality restraints: 4408 Sorted by residual: chirality pdb=" CBH Y01 D1204 " pdb=" CAT Y01 D1204 " pdb=" CAZ Y01 D1204 " pdb=" CBF Y01 D1204 " both_signs ideal model delta sigma weight residual False -2.85 -3.28 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CBH Y01 B1204 " pdb=" CAT Y01 B1204 " pdb=" CAZ Y01 B1204 " pdb=" CBF Y01 B1204 " both_signs ideal model delta sigma weight residual False -2.85 -3.28 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CBH Y01 C1204 " pdb=" CAT Y01 C1204 " pdb=" CAZ Y01 C1204 " pdb=" CBF Y01 C1204 " both_signs ideal model delta sigma weight residual False -2.85 -3.28 0.43 2.00e-01 2.50e+01 4.61e+00 ... (remaining 4405 not shown) Planarity restraints: 8112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 168 " -0.060 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO C 169 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO C 169 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 169 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 168 " 0.060 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO A 169 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 168 " 0.060 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO D 169 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 169 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 169 " 0.049 5.00e-02 4.00e+02 ... (remaining 8109 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 2652 2.19 - 2.79: 110359 2.79 - 3.39: 148878 3.39 - 4.00: 184213 4.00 - 4.60: 297333 Nonbonded interactions: 743435 Sorted by model distance: nonbonded pdb=" OE1 GLU C 501 " pdb=" H GLU C 501 " model vdw 1.587 2.450 nonbonded pdb=" OE1 GLU D 501 " pdb=" H GLU D 501 " model vdw 1.587 2.450 nonbonded pdb=" OE1 GLU B 501 " pdb=" H GLU B 501 " model vdw 1.587 2.450 nonbonded pdb=" OE1 GLU A 501 " pdb=" H GLU A 501 " model vdw 1.588 2.450 nonbonded pdb=" OE1 GLU B 321 " pdb=" H GLU B 321 " model vdw 1.611 2.450 ... (remaining 743430 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: 0.19 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 4.690 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: 0.750 Extract box with map and model: 1.740 Check model and map are aligned: 0.320 Set scattering table: 0.400 Process input model: 109.380 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 28920 Z= 0.358 Angle : 0.788 12.910 39284 Z= 0.332 Chirality : 0.054 0.431 4408 Planarity : 0.004 0.090 4808 Dihedral : 12.459 74.548 11248 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.17 % Allowed : 9.79 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.15), residues: 3336 helix: 2.47 (0.11), residues: 2188 sheet: -1.36 (0.38), residues: 200 loop : -1.23 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 831 HIS 0.004 0.001 HIS A 431 PHE 0.011 0.001 PHE C 639 TYR 0.006 0.001 TYR B 294 ARG 0.010 0.000 ARG D1087 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 267 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 ASP cc_start: 0.8888 (m-30) cc_final: 0.8300 (t0) REVERT: B 675 ASP cc_start: 0.8881 (m-30) cc_final: 0.8295 (t0) REVERT: D 675 ASP cc_start: 0.8879 (m-30) cc_final: 0.8295 (t0) REVERT: C 675 ASP cc_start: 0.8880 (m-30) cc_final: 0.8293 (t0) outliers start: 5 outliers final: 4 residues processed: 267 average time/residue: 0.6688 time to fit residues: 292.0936 Evaluate side-chains 246 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 242 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain D residue 148 HIS Chi-restraints excluded: chain C residue 148 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 266 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 308 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 164 ASN ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN B 145 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN B 462 ASN D 145 GLN D 164 ASN C 145 GLN C 164 ASN C 327 ASN C 462 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.149075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.095492 restraints weight = 125039.847| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.50 r_work: 0.3134 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28920 Z= 0.283 Angle : 0.543 7.164 39284 Z= 0.295 Chirality : 0.037 0.154 4408 Planarity : 0.004 0.061 4808 Dihedral : 7.338 61.285 4884 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.02 % Allowed : 9.96 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.15), residues: 3336 helix: 2.27 (0.11), residues: 2276 sheet: -1.39 (0.37), residues: 188 loop : -1.43 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 831 HIS 0.004 0.001 HIS A 569 PHE 0.019 0.001 PHE B1088 TYR 0.008 0.001 TYR B 294 ARG 0.003 0.000 ARG C 907 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 3.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8404 (p) REVERT: A 786 PHE cc_start: 0.7683 (m-10) cc_final: 0.6621 (t80) REVERT: B 151 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8404 (p) REVERT: B 786 PHE cc_start: 0.7676 (m-10) cc_final: 0.6612 (t80) REVERT: D 151 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8394 (p) REVERT: D 786 PHE cc_start: 0.7674 (m-10) cc_final: 0.6611 (t80) REVERT: C 151 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8396 (p) REVERT: C 786 PHE cc_start: 0.7674 (m-10) cc_final: 0.6614 (t80) outliers start: 30 outliers final: 22 residues processed: 287 average time/residue: 0.7576 time to fit residues: 340.7333 Evaluate side-chains 262 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 815 TYR Chi-restraints excluded: chain D residue 145 GLN Chi-restraints excluded: chain D residue 148 HIS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 815 TYR Chi-restraints excluded: chain C residue 145 GLN Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 815 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 186 optimal weight: 9.9990 chunk 286 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 278 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 164 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 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 = 0.4036 r_free = 0.4036 target = 0.149019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.094555 restraints weight = 125437.577| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.53 r_work: 0.3117 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28920 Z= 0.228 Angle : 0.497 8.834 39284 Z= 0.271 Chirality : 0.036 0.144 4408 Planarity : 0.004 0.054 4808 Dihedral : 7.359 60.479 4884 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.19 % Allowed : 9.62 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.15), residues: 3336 helix: 2.22 (0.11), residues: 2276 sheet: -1.52 (0.36), residues: 188 loop : -1.44 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 390 HIS 0.003 0.001 HIS D 146 PHE 0.013 0.001 PHE B 175 TYR 0.009 0.001 TYR B 294 ARG 0.003 0.000 ARG A1087 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 248 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8366 (p) REVERT: A 171 MET cc_start: 0.7272 (tpp) cc_final: 0.6994 (tpp) REVERT: A 699 ASP cc_start: 0.7867 (t70) cc_final: 0.7648 (t0) REVERT: A 750 TRP cc_start: 0.7334 (m100) cc_final: 0.6698 (t60) REVERT: A 786 PHE cc_start: 0.7754 (m-10) cc_final: 0.6633 (t80) REVERT: B 151 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8352 (p) REVERT: B 171 MET cc_start: 0.7251 (tpp) cc_final: 0.6960 (tpp) REVERT: B 327 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8284 (t0) REVERT: B 390 TRP cc_start: 0.7377 (m100) cc_final: 0.7038 (m100) REVERT: B 699 ASP cc_start: 0.7853 (t70) cc_final: 0.7637 (t0) REVERT: B 750 TRP cc_start: 0.7326 (m100) cc_final: 0.6691 (t60) REVERT: B 786 PHE cc_start: 0.7691 (m-10) cc_final: 0.6558 (t80) REVERT: D 151 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8356 (p) REVERT: D 171 MET cc_start: 0.7234 (tpp) cc_final: 0.6947 (tpp) REVERT: D 699 ASP cc_start: 0.7850 (t70) cc_final: 0.7630 (t0) REVERT: D 750 TRP cc_start: 0.7335 (m100) cc_final: 0.6694 (t60) REVERT: D 786 PHE cc_start: 0.7685 (m-10) cc_final: 0.6549 (t80) REVERT: C 151 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8361 (p) REVERT: C 171 MET cc_start: 0.7235 (tpp) cc_final: 0.6947 (tpp) REVERT: C 327 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8282 (t0) REVERT: C 390 TRP cc_start: 0.7383 (m100) cc_final: 0.7047 (m100) REVERT: C 533 PHE cc_start: 0.8732 (t80) cc_final: 0.8510 (t80) REVERT: C 699 ASP cc_start: 0.7851 (t70) cc_final: 0.7634 (t0) REVERT: C 750 TRP cc_start: 0.7338 (m100) cc_final: 0.6701 (t60) REVERT: C 786 PHE cc_start: 0.7685 (m-10) cc_final: 0.6552 (t80) outliers start: 35 outliers final: 17 residues processed: 275 average time/residue: 0.7669 time to fit residues: 329.9416 Evaluate side-chains 266 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 243 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 815 TYR Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain D residue 148 HIS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 815 TYR Chi-restraints excluded: chain D residue 866 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 815 TYR Chi-restraints excluded: chain C residue 866 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 147 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 311 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 329 optimal weight: 0.0470 chunk 302 optimal weight: 9.9990 chunk 275 optimal weight: 0.0170 chunk 243 optimal weight: 2.9990 chunk 322 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 307 optimal weight: 4.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.149134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.095090 restraints weight = 125136.919| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.49 r_work: 0.3125 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28920 Z= 0.169 Angle : 0.452 4.927 39284 Z= 0.248 Chirality : 0.035 0.141 4408 Planarity : 0.003 0.052 4808 Dihedral : 7.234 59.831 4884 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.19 % Allowed : 9.76 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.15), residues: 3336 helix: 2.32 (0.11), residues: 2276 sheet: -1.53 (0.37), residues: 188 loop : -1.48 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 831 HIS 0.002 0.001 HIS A 146 PHE 0.012 0.001 PHE B 175 TYR 0.008 0.001 TYR B 294 ARG 0.002 0.000 ARG A1087 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Evaluate side-chains 289 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8335 (p) REVERT: A 750 TRP cc_start: 0.7365 (m100) cc_final: 0.6763 (t60) REVERT: A 786 PHE cc_start: 0.7664 (m-10) cc_final: 0.6574 (t80) REVERT: B 151 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8325 (p) REVERT: B 750 TRP cc_start: 0.7358 (m100) cc_final: 0.6758 (t60) REVERT: D 151 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8325 (p) REVERT: D 750 TRP cc_start: 0.7368 (m100) cc_final: 0.6766 (t60) REVERT: C 151 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8328 (p) REVERT: C 750 TRP cc_start: 0.7364 (m100) cc_final: 0.6764 (t60) outliers start: 35 outliers final: 25 residues processed: 281 average time/residue: 0.8481 time to fit residues: 378.2893 Evaluate side-chains 273 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 815 TYR Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain D residue 148 HIS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain D residue 815 TYR Chi-restraints excluded: chain D residue 866 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 539 GLU Chi-restraints excluded: chain C residue 815 TYR Chi-restraints excluded: chain C residue 866 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 113 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 251 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 274 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.146324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.091693 restraints weight = 125926.661| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.48 r_work: 0.3062 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28920 Z= 0.286 Angle : 0.499 5.117 39284 Z= 0.274 Chirality : 0.037 0.140 4408 Planarity : 0.004 0.069 4808 Dihedral : 7.134 56.776 4884 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.63 % Allowed : 10.40 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.54 (0.15), residues: 3336 helix: 2.20 (0.11), residues: 2264 sheet: -1.66 (0.37), residues: 188 loop : -1.58 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 831 HIS 0.003 0.001 HIS A 431 PHE 0.017 0.001 PHE A 175 TYR 0.011 0.001 TYR C 832 ARG 0.008 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Evaluate side-chains 290 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8364 (p) REVERT: A 539 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6395 (mp0) REVERT: A 750 TRP cc_start: 0.7466 (m100) cc_final: 0.6894 (t60) REVERT: A 786 PHE cc_start: 0.7870 (m-10) cc_final: 0.6701 (t80) REVERT: B 151 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8387 (p) REVERT: B 539 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6407 (mp0) REVERT: B 750 TRP cc_start: 0.7469 (m100) cc_final: 0.6890 (t60) REVERT: B 786 PHE cc_start: 0.7866 (m-10) cc_final: 0.6701 (t80) REVERT: D 151 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8389 (p) REVERT: D 539 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6395 (mp0) REVERT: D 750 TRP cc_start: 0.7477 (m100) cc_final: 0.6900 (t60) REVERT: D 786 PHE cc_start: 0.7857 (m-10) cc_final: 0.6695 (t80) REVERT: C 151 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8398 (p) REVERT: C 539 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6388 (mp0) REVERT: C 750 TRP cc_start: 0.7457 (m100) cc_final: 0.6883 (t60) REVERT: C 786 PHE cc_start: 0.7860 (m-10) cc_final: 0.6696 (t80) outliers start: 48 outliers final: 31 residues processed: 282 average time/residue: 0.7464 time to fit residues: 330.0807 Evaluate side-chains 276 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 237 time to evaluate : 3.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 815 TYR Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain D residue 148 HIS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 815 TYR Chi-restraints excluded: chain D residue 866 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 313 CYS Chi-restraints excluded: chain C residue 539 GLU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 815 TYR Chi-restraints excluded: chain C residue 866 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 274 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 325 optimal weight: 0.3980 chunk 212 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 280 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 226 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.145874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.091443 restraints weight = 125763.876| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.47 r_work: 0.3057 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28920 Z= 0.277 Angle : 0.488 5.337 39284 Z= 0.268 Chirality : 0.037 0.144 4408 Planarity : 0.003 0.048 4808 Dihedral : 7.158 56.830 4884 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.25 % Allowed : 11.14 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.15), residues: 3336 helix: 2.18 (0.11), residues: 2260 sheet: -1.79 (0.36), residues: 188 loop : -1.63 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 831 HIS 0.002 0.001 HIS C 431 PHE 0.016 0.001 PHE A 175 TYR 0.010 0.001 TYR A 832 ARG 0.003 0.000 ARG A1087 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8524 (p) REVERT: A 196 TYR cc_start: 0.8291 (m-80) cc_final: 0.7829 (m-80) REVERT: A 750 TRP cc_start: 0.7491 (m100) cc_final: 0.6889 (t60) REVERT: A 786 PHE cc_start: 0.7901 (m-10) cc_final: 0.6702 (t80) REVERT: B 151 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8479 (p) REVERT: B 196 TYR cc_start: 0.8295 (m-80) cc_final: 0.7840 (m-80) REVERT: B 750 TRP cc_start: 0.7455 (m100) cc_final: 0.6865 (t60) REVERT: D 151 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8489 (p) REVERT: D 196 TYR cc_start: 0.8284 (m-80) cc_final: 0.7821 (m-80) REVERT: D 750 TRP cc_start: 0.7471 (m100) cc_final: 0.6876 (t60) REVERT: C 151 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8486 (p) REVERT: C 196 TYR cc_start: 0.8289 (m-80) cc_final: 0.7828 (m-80) REVERT: C 750 TRP cc_start: 0.7447 (m100) cc_final: 0.6866 (t60) outliers start: 37 outliers final: 28 residues processed: 275 average time/residue: 0.7557 time to fit residues: 325.9148 Evaluate side-chains 266 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 3.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 815 TYR Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain D residue 148 HIS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 815 TYR Chi-restraints excluded: chain D residue 866 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 313 CYS Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 815 TYR Chi-restraints excluded: chain C residue 866 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 15 optimal weight: 4.9990 chunk 276 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 193 optimal weight: 0.0270 chunk 61 optimal weight: 3.9990 chunk 316 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 271 optimal weight: 7.9990 chunk 310 optimal weight: 1.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.146651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.091755 restraints weight = 125872.197| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.53 r_work: 0.3064 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28920 Z= 0.222 Angle : 0.462 4.274 39284 Z= 0.254 Chirality : 0.036 0.140 4408 Planarity : 0.004 0.062 4808 Dihedral : 7.101 55.539 4884 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.39 % Allowed : 11.21 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.15), residues: 3336 helix: 2.23 (0.11), residues: 2260 sheet: -1.73 (0.37), residues: 188 loop : -1.57 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 831 HIS 0.004 0.001 HIS B 431 PHE 0.014 0.001 PHE A 175 TYR 0.010 0.001 TYR A 832 ARG 0.004 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 3.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8483 (p) REVERT: A 196 TYR cc_start: 0.8302 (m-80) cc_final: 0.7820 (m-80) REVERT: A 539 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: A 750 TRP cc_start: 0.7514 (m100) cc_final: 0.6886 (t60) REVERT: B 151 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8480 (p) REVERT: B 196 TYR cc_start: 0.8300 (m-80) cc_final: 0.7818 (m-80) REVERT: B 539 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: B 750 TRP cc_start: 0.7509 (m100) cc_final: 0.6884 (t60) REVERT: B 786 PHE cc_start: 0.7852 (m-10) cc_final: 0.6624 (t80) REVERT: D 151 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8484 (p) REVERT: D 196 TYR cc_start: 0.8290 (m-80) cc_final: 0.7811 (m-80) REVERT: D 539 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: D 750 TRP cc_start: 0.7517 (m100) cc_final: 0.6884 (t60) REVERT: D 786 PHE cc_start: 0.7842 (m-10) cc_final: 0.6619 (t80) REVERT: C 151 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8491 (p) REVERT: C 196 TYR cc_start: 0.8294 (m-80) cc_final: 0.7818 (m-80) REVERT: C 539 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: C 750 TRP cc_start: 0.7503 (m100) cc_final: 0.6883 (t60) REVERT: C 786 PHE cc_start: 0.7842 (m-10) cc_final: 0.6618 (t80) outliers start: 41 outliers final: 25 residues processed: 267 average time/residue: 0.7586 time to fit residues: 321.3008 Evaluate side-chains 266 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 815 TYR Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain D residue 148 HIS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 815 TYR Chi-restraints excluded: chain D residue 866 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 539 GLU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 815 TYR Chi-restraints excluded: chain C residue 866 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 313 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 246 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 291 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.145297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.090725 restraints weight = 126697.976| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.50 r_work: 0.3041 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 28920 Z= 0.307 Angle : 0.503 5.335 39284 Z= 0.278 Chirality : 0.037 0.139 4408 Planarity : 0.004 0.053 4808 Dihedral : 7.219 54.589 4884 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.15 % Allowed : 11.72 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.15), residues: 3336 helix: 2.12 (0.11), residues: 2260 sheet: -1.85 (0.37), residues: 188 loop : -1.65 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 831 HIS 0.002 0.001 HIS B 267 PHE 0.016 0.001 PHE A 175 TYR 0.011 0.001 TYR D 832 ARG 0.003 0.000 ARG A1004 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 3.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8447 (p) REVERT: A 196 TYR cc_start: 0.8338 (m-80) cc_final: 0.7841 (m-80) REVERT: A 750 TRP cc_start: 0.7535 (m100) cc_final: 0.6831 (t60) REVERT: B 151 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8440 (p) REVERT: B 750 TRP cc_start: 0.7531 (m100) cc_final: 0.6782 (t60) REVERT: D 151 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8449 (p) REVERT: D 196 TYR cc_start: 0.8324 (m-80) cc_final: 0.7830 (m-80) REVERT: D 750 TRP cc_start: 0.7538 (m100) cc_final: 0.6787 (t60) REVERT: C 151 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8454 (p) REVERT: C 196 TYR cc_start: 0.8326 (m-80) cc_final: 0.7833 (m-80) REVERT: C 750 TRP cc_start: 0.7522 (m100) cc_final: 0.6786 (t60) outliers start: 34 outliers final: 30 residues processed: 263 average time/residue: 0.7591 time to fit residues: 315.4216 Evaluate side-chains 268 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 815 TYR Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain D residue 148 HIS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 815 TYR Chi-restraints excluded: chain D residue 866 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 815 TYR Chi-restraints excluded: chain C residue 866 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 336 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 236 optimal weight: 0.9990 chunk 258 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 317 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 259 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 280 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.146149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.091999 restraints weight = 126262.237| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.50 r_work: 0.3062 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28920 Z= 0.216 Angle : 0.465 4.200 39284 Z= 0.257 Chirality : 0.036 0.139 4408 Planarity : 0.004 0.050 4808 Dihedral : 7.210 57.817 4884 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.12 % Allowed : 11.72 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.53 (0.15), residues: 3336 helix: 2.23 (0.11), residues: 2260 sheet: -1.80 (0.37), residues: 188 loop : -1.62 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 831 HIS 0.002 0.000 HIS A 431 PHE 0.013 0.001 PHE A 175 TYR 0.011 0.001 TYR D 832 ARG 0.003 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 3.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8417 (p) REVERT: A 196 TYR cc_start: 0.8306 (m-80) cc_final: 0.7770 (m-80) REVERT: A 750 TRP cc_start: 0.7470 (m100) cc_final: 0.6823 (t60) REVERT: B 151 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8461 (p) REVERT: B 750 TRP cc_start: 0.7447 (m100) cc_final: 0.6814 (t60) REVERT: D 151 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8467 (p) REVERT: D 196 TYR cc_start: 0.8299 (m-80) cc_final: 0.7795 (m-80) REVERT: D 750 TRP cc_start: 0.7450 (m100) cc_final: 0.6821 (t60) REVERT: C 151 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8468 (p) REVERT: C 196 TYR cc_start: 0.8289 (m-80) cc_final: 0.7759 (m-80) REVERT: C 750 TRP cc_start: 0.7441 (m100) cc_final: 0.6817 (t60) outliers start: 33 outliers final: 29 residues processed: 266 average time/residue: 0.7685 time to fit residues: 324.0973 Evaluate side-chains 268 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 815 TYR Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain D residue 148 HIS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 815 TYR Chi-restraints excluded: chain D residue 866 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 815 TYR Chi-restraints excluded: chain C residue 866 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 244 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 277 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.145657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.090843 restraints weight = 126538.293| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.52 r_work: 0.3051 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28920 Z= 0.266 Angle : 0.480 4.326 39284 Z= 0.265 Chirality : 0.037 0.141 4408 Planarity : 0.004 0.047 4808 Dihedral : 7.342 58.680 4884 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.08 % Allowed : 11.79 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.15), residues: 3336 helix: 2.16 (0.11), residues: 2264 sheet: -1.85 (0.36), residues: 188 loop : -1.67 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 831 HIS 0.002 0.000 HIS B 267 PHE 0.015 0.001 PHE A 175 TYR 0.010 0.001 TYR D 832 ARG 0.003 0.000 ARG A 374 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue LEU 130 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue THR 375 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue TYR 526 is missing expected H atoms. Skipping. Residue LEU 735 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 856 is missing expected H atoms. Skipping. Residue MET 1065 is missing expected H atoms. Skipping. Residue LYS 1099 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8440 (p) REVERT: A 196 TYR cc_start: 0.8326 (m-80) cc_final: 0.7797 (m-80) REVERT: A 750 TRP cc_start: 0.7506 (m100) cc_final: 0.6810 (t60) REVERT: B 151 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8431 (p) REVERT: B 750 TRP cc_start: 0.7506 (m100) cc_final: 0.6801 (t60) REVERT: D 151 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8440 (p) REVERT: D 196 TYR cc_start: 0.8309 (m-80) cc_final: 0.7785 (m-80) REVERT: D 750 TRP cc_start: 0.7508 (m100) cc_final: 0.6807 (t60) REVERT: C 151 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8441 (p) REVERT: C 196 TYR cc_start: 0.8310 (m-80) cc_final: 0.7785 (m-80) REVERT: C 750 TRP cc_start: 0.7489 (m100) cc_final: 0.6801 (t60) outliers start: 32 outliers final: 28 residues processed: 249 average time/residue: 0.8405 time to fit residues: 333.5776 Evaluate side-chains 259 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 227 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 815 TYR Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain D residue 148 HIS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 815 TYR Chi-restraints excluded: chain D residue 866 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 815 TYR Chi-restraints excluded: chain C residue 866 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 286 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 288 optimal weight: 0.8980 chunk 291 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.145660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.090855 restraints weight = 126672.570| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.51 r_work: 0.3052 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 28920 Z= 0.255 Angle : 0.478 12.045 39284 Z= 0.262 Chirality : 0.037 0.139 4408 Planarity : 0.004 0.046 4808 Dihedral : 7.315 59.528 4884 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.32 % Allowed : 11.69 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.15), residues: 3336 helix: 2.17 (0.11), residues: 2264 sheet: -1.84 (0.36), residues: 188 loop : -1.68 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 831 HIS 0.002 0.001 HIS D 431 PHE 0.014 0.001 PHE B 175 TYR 0.011 0.001 TYR D 832 ARG 0.003 0.000 ARG A 374 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25292.55 seconds wall clock time: 431 minutes 26.69 seconds (25886.69 seconds total)