Starting phenix.real_space_refine on Wed Sep 25 18:03:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6i_44260/09_2024/9b6i_44260_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6i_44260/09_2024/9b6i_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6i_44260/09_2024/9b6i_44260.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6i_44260/09_2024/9b6i_44260.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6i_44260/09_2024/9b6i_44260_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6i_44260/09_2024/9b6i_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): 0.74s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 37.89, 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: 11.00 Conformation dependent library (CDL) restraints added in 3.3 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: 3.17 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: 18.89 Time building geometry restraints manager: 13.54 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 4.520 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: 0.720 Extract box with map and model: 1.560 Check model and map are aligned: 0.310 Set scattering table: 0.390 Process input model: 106.580 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.110 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:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.800 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 5 poor density : 267 time to evaluate : 3.966 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: 0.6708 time to fit residues: 294.5551 Evaluate side-chains 246 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 242 time to evaluate : 3.162 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 fitting. rotamer outliers: 30 poor density : 265 time to evaluate : 3.250 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: 0.8744 (OUTLIER) cc_final: 0.8347 (p) REVERT: A 786 PHE cc_start: 0.7492 (m-10) cc_final: 0.6878 (t80) REVERT: B 151 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8345 (p) REVERT: B 786 PHE cc_start: 0.7491 (m-10) cc_final: 0.6875 (t80) REVERT: D 151 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8344 (p) REVERT: D 786 PHE cc_start: 0.7488 (m-10) cc_final: 0.6873 (t80) REVERT: C 151 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8345 (p) REVERT: C 786 PHE cc_start: 0.7486 (m-10) cc_final: 0.6871 (t80) outliers start: 30 outliers final: 22 residues processed: 287 average time/residue: 0.8010 time to fit residues: 363.3891 Evaluate side-chains 262 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 236 time to evaluate : 3.247 ------------------------------------------------------------------------------- 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 171 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 256 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 309 optimal weight: 1.9990 chunk 334 optimal weight: 2.9990 chunk 275 optimal weight: 4.9990 chunk 306 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 28920 Z= 0.390 Angle : 0.567 8.667 39284 Z= 0.310 Chirality : 0.039 0.147 4408 Planarity : 0.004 0.055 4808 Dihedral : 7.396 59.514 4884 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.56 % Allowed : 9.49 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.14), residues: 3336 helix: 1.95 (0.11), residues: 2268 sheet: -1.67 (0.36), residues: 188 loop : -1.53 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 831 HIS 0.003 0.001 HIS D1086 PHE 0.018 0.002 PHE A 175 TYR 0.011 0.001 TYR B 294 ARG 0.004 0.000 ARG A1004 *********************** 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 286 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 240 time to evaluate : 3.210 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: 0.8814 (OUTLIER) cc_final: 0.8416 (p) REVERT: A 171 MET cc_start: 0.7682 (tpp) cc_final: 0.7400 (tpp) REVERT: A 196 TYR cc_start: 0.8163 (m-80) cc_final: 0.7881 (m-80) REVERT: A 786 PHE cc_start: 0.7686 (m-10) cc_final: 0.6932 (t80) REVERT: B 151 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8411 (p) REVERT: B 171 MET cc_start: 0.7666 (tpp) cc_final: 0.7381 (tpp) REVERT: B 327 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8681 (t0) REVERT: B 786 PHE cc_start: 0.7681 (m-10) cc_final: 0.6932 (t80) REVERT: D 151 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8412 (p) REVERT: D 171 MET cc_start: 0.7635 (tpp) cc_final: 0.7344 (tpp) REVERT: D 196 TYR cc_start: 0.8212 (m-80) cc_final: 0.7915 (m-80) REVERT: D 786 PHE cc_start: 0.7682 (m-10) cc_final: 0.6933 (t80) REVERT: C 151 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8412 (p) REVERT: C 171 MET cc_start: 0.7634 (tpp) cc_final: 0.7344 (tpp) REVERT: C 196 TYR cc_start: 0.8213 (m-80) cc_final: 0.7916 (m-80) REVERT: C 327 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8682 (t0) REVERT: C 786 PHE cc_start: 0.7676 (m-10) cc_final: 0.6929 (t80) outliers start: 46 outliers final: 24 residues processed: 279 average time/residue: 0.7681 time to fit residues: 335.4629 Evaluate side-chains 262 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 232 time to evaluate : 3.221 ------------------------------------------------------------------------------- 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 313 CYS 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 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 224 ILE Chi-restraints excluded: chain D residue 313 CYS 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 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 305 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 160 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 310 optimal weight: 1.9990 chunk 328 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28920 Z= 0.184 Angle : 0.464 5.105 39284 Z= 0.254 Chirality : 0.035 0.143 4408 Planarity : 0.003 0.052 4808 Dihedral : 7.142 58.735 4884 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.22 % Allowed : 10.20 % Favored : 88.58 % 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: 1.59 (0.15), residues: 3336 helix: 2.22 (0.11), residues: 2264 sheet: -1.65 (0.36), residues: 188 loop : -1.49 (0.19), residues: 884 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 0.014 0.001 PHE A 639 TYR 0.009 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 276 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 240 time to evaluate : 3.222 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: A 151 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8301 (p) REVERT: A 171 MET cc_start: 0.7612 (tpp) cc_final: 0.7339 (tpp) REVERT: A 340 GLU cc_start: 0.7183 (tt0) cc_final: 0.6868 (tt0) REVERT: A 786 PHE cc_start: 0.7664 (m-10) cc_final: 0.6928 (t80) REVERT: B 151 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8266 (p) REVERT: B 171 MET cc_start: 0.7597 (tpp) cc_final: 0.7322 (tpp) REVERT: B 340 GLU cc_start: 0.7192 (tt0) cc_final: 0.6877 (tt0) REVERT: B 786 PHE cc_start: 0.7596 (m-10) cc_final: 0.6841 (t80) REVERT: D 151 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8266 (p) REVERT: D 171 MET cc_start: 0.7596 (tpp) cc_final: 0.7321 (tpp) REVERT: D 340 GLU cc_start: 0.7193 (tt0) cc_final: 0.6876 (tt0) REVERT: D 786 PHE cc_start: 0.7596 (m-10) cc_final: 0.6841 (t80) REVERT: C 151 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8267 (p) REVERT: C 171 MET cc_start: 0.7595 (tpp) cc_final: 0.7319 (tpp) REVERT: C 340 GLU cc_start: 0.7190 (tt0) cc_final: 0.6875 (tt0) REVERT: C 786 PHE cc_start: 0.7591 (m-10) cc_final: 0.6839 (t80) outliers start: 36 outliers final: 28 residues processed: 270 average time/residue: 0.7710 time to fit residues: 325.9361 Evaluate side-chains 262 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 230 time to evaluate : 2.889 ------------------------------------------------------------------------------- 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 194 THR Chi-restraints excluded: chain A residue 224 ILE 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 327 ASN 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 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 327 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 280 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 294 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 28920 Z= 0.326 Angle : 0.517 5.196 39284 Z= 0.282 Chirality : 0.038 0.140 4408 Planarity : 0.004 0.062 4808 Dihedral : 7.153 59.588 4884 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.59 % Allowed : 10.81 % 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: 1.40 (0.15), residues: 3336 helix: 2.11 (0.11), residues: 2260 sheet: -1.78 (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 C 831 HIS 0.002 0.001 HIS A 431 PHE 0.017 0.001 PHE B 175 TYR 0.011 0.001 TYR A 832 ARG 0.003 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 282 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 235 time to evaluate : 3.206 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: 0.8761 (OUTLIER) cc_final: 0.8352 (p) REVERT: A 171 MET cc_start: 0.7561 (tpp) cc_final: 0.7336 (tpp) REVERT: A 196 TYR cc_start: 0.8165 (m-80) cc_final: 0.7865 (m-80) REVERT: A 340 GLU cc_start: 0.7257 (tt0) cc_final: 0.6962 (tt0) REVERT: B 151 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8349 (p) REVERT: B 171 MET cc_start: 0.7505 (tpp) cc_final: 0.7281 (tpp) REVERT: B 340 GLU cc_start: 0.7264 (tt0) cc_final: 0.6969 (tt0) REVERT: B 943 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8891 (mtmm) REVERT: D 151 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8352 (p) REVERT: D 171 MET cc_start: 0.7503 (tpp) cc_final: 0.7280 (tpp) REVERT: D 196 TYR cc_start: 0.8158 (m-80) cc_final: 0.7856 (m-80) REVERT: D 340 GLU cc_start: 0.7262 (tt0) cc_final: 0.6970 (tt0) REVERT: D 943 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8894 (mtmm) REVERT: C 151 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8351 (p) REVERT: C 171 MET cc_start: 0.7501 (tpp) cc_final: 0.7279 (tpp) REVERT: C 196 TYR cc_start: 0.8160 (m-80) cc_final: 0.7859 (m-80) REVERT: C 340 GLU cc_start: 0.7261 (tt0) cc_final: 0.6968 (tt0) REVERT: C 943 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8894 (mtmm) outliers start: 47 outliers final: 32 residues processed: 274 average time/residue: 0.7744 time to fit residues: 335.2786 Evaluate side-chains 258 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 219 time to evaluate : 3.195 ------------------------------------------------------------------------------- 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 194 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 B residue 943 LYS 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 571 LEU Chi-restraints excluded: chain D residue 815 TYR Chi-restraints excluded: chain D residue 866 LEU Chi-restraints excluded: chain D residue 943 LYS 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 571 LEU Chi-restraints excluded: chain C residue 815 TYR Chi-restraints excluded: chain C residue 866 LEU Chi-restraints excluded: chain C residue 943 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 328 optimal weight: 0.8980 chunk 273 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 28920 Z= 0.292 Angle : 0.493 5.338 39284 Z= 0.271 Chirality : 0.037 0.140 4408 Planarity : 0.004 0.049 4808 Dihedral : 7.167 55.471 4884 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.49 % Allowed : 11.48 % Favored : 87.03 % 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: 1.38 (0.15), residues: 3336 helix: 2.10 (0.11), residues: 2260 sheet: -1.87 (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 C 831 HIS 0.005 0.001 HIS A 431 PHE 0.015 0.001 PHE B 175 TYR 0.011 0.001 TYR D 832 ARG 0.002 0.000 ARG D1087 *********************** 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 277 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 233 time to evaluate : 3.203 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: 0.8746 (OUTLIER) cc_final: 0.8464 (p) REVERT: A 171 MET cc_start: 0.7486 (tpp) cc_final: 0.7285 (tpp) REVERT: A 340 GLU cc_start: 0.7253 (tt0) cc_final: 0.6950 (tt0) REVERT: A 539 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: B 151 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8426 (p) REVERT: B 171 MET cc_start: 0.7487 (tpp) cc_final: 0.7286 (tpp) REVERT: B 340 GLU cc_start: 0.7260 (tt0) cc_final: 0.6960 (tt0) REVERT: B 539 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: B 943 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8916 (mtmm) REVERT: D 151 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8426 (p) REVERT: D 171 MET cc_start: 0.7487 (tpp) cc_final: 0.7286 (tpp) REVERT: D 340 GLU cc_start: 0.7263 (tt0) cc_final: 0.6966 (tt0) REVERT: D 539 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: D 943 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8920 (mtmm) REVERT: C 151 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8429 (p) REVERT: C 171 MET cc_start: 0.7484 (tpp) cc_final: 0.7282 (tpp) REVERT: C 340 GLU cc_start: 0.7261 (tt0) cc_final: 0.6961 (tt0) REVERT: C 539 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: C 943 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8918 (mtmm) outliers start: 44 outliers final: 29 residues processed: 269 average time/residue: 0.7896 time to fit residues: 336.9271 Evaluate side-chains 265 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 225 time to evaluate : 3.228 ------------------------------------------------------------------------------- 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 194 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 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 B residue 943 LYS 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 D residue 943 LYS 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 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 Chi-restraints excluded: chain C residue 943 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 240 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 chunk 276 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 327 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28920 Z= 0.196 Angle : 0.453 5.345 39284 Z= 0.249 Chirality : 0.035 0.139 4408 Planarity : 0.004 0.064 4808 Dihedral : 7.059 55.412 4884 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.52 % Allowed : 11.45 % Favored : 87.03 % 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: 1.55 (0.15), residues: 3336 helix: 2.22 (0.11), residues: 2264 sheet: -1.82 (0.37), residues: 188 loop : -1.57 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 831 HIS 0.003 0.000 HIS B 431 PHE 0.012 0.001 PHE B 175 TYR 0.010 0.001 TYR D 832 ARG 0.002 0.000 ARG A1087 *********************** 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 279 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 234 time to evaluate : 3.280 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: A 151 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8438 (p) REVERT: A 196 TYR cc_start: 0.8179 (m-80) cc_final: 0.7843 (m-80) REVERT: A 340 GLU cc_start: 0.7305 (tt0) cc_final: 0.7002 (tt0) REVERT: A 539 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: B 151 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8435 (p) REVERT: B 340 GLU cc_start: 0.7304 (tt0) cc_final: 0.7003 (tt0) REVERT: B 539 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: D 151 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8433 (p) REVERT: D 196 TYR cc_start: 0.8167 (m-80) cc_final: 0.7833 (m-80) REVERT: D 340 GLU cc_start: 0.7310 (tt0) cc_final: 0.7037 (tt0) REVERT: D 539 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: C 151 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8435 (p) REVERT: C 196 TYR cc_start: 0.8169 (m-80) cc_final: 0.7835 (m-80) REVERT: C 340 GLU cc_start: 0.7305 (tt0) cc_final: 0.7000 (tt0) REVERT: C 539 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7056 (mp0) outliers start: 45 outliers final: 32 residues processed: 264 average time/residue: 0.7751 time to fit residues: 320.4736 Evaluate side-chains 255 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 215 time to evaluate : 3.220 ------------------------------------------------------------------------------- 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 224 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 472 MET 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 352 LEU 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 352 LEU 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 352 LEU 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 202 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 257 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28920 Z= 0.197 Angle : 0.450 5.335 39284 Z= 0.247 Chirality : 0.035 0.137 4408 Planarity : 0.003 0.054 4808 Dihedral : 6.998 55.164 4884 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.49 % Allowed : 11.48 % Favored : 87.03 % 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: 1.62 (0.15), residues: 3336 helix: 2.31 (0.11), residues: 2256 sheet: -1.82 (0.37), residues: 188 loop : -1.61 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 831 HIS 0.002 0.000 HIS D 431 PHE 0.013 0.001 PHE C 175 TYR 0.010 0.001 TYR C 832 ARG 0.002 0.000 ARG C1087 *********************** 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 269 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 225 time to evaluate : 3.190 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: 0.8670 (OUTLIER) cc_final: 0.8398 (p) REVERT: A 196 TYR cc_start: 0.8217 (m-80) cc_final: 0.7859 (m-80) REVERT: A 539 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: B 151 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8385 (p) REVERT: B 539 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: D 151 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8385 (p) REVERT: D 196 TYR cc_start: 0.8207 (m-80) cc_final: 0.7849 (m-80) REVERT: D 539 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: C 151 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8384 (p) REVERT: C 196 TYR cc_start: 0.8208 (m-80) cc_final: 0.7851 (m-80) REVERT: C 539 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7055 (mp0) outliers start: 44 outliers final: 35 residues processed: 253 average time/residue: 0.8119 time to fit residues: 328.1029 Evaluate side-chains 261 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 218 time to evaluate : 3.192 ------------------------------------------------------------------------------- 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 194 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 472 MET 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 352 LEU Chi-restraints excluded: chain B residue 472 MET 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 352 LEU Chi-restraints excluded: chain D residue 472 MET 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 352 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 7.9990 chunk 313 optimal weight: 8.9990 chunk 286 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 239 optimal weight: 0.0030 chunk 93 optimal weight: 5.9990 chunk 275 optimal weight: 8.9990 chunk 288 optimal weight: 6.9990 chunk 304 optimal weight: 0.9980 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28920 Z= 0.287 Angle : 0.482 4.423 39284 Z= 0.265 Chirality : 0.037 0.142 4408 Planarity : 0.004 0.070 4808 Dihedral : 7.153 54.372 4884 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.42 % Allowed : 11.82 % Favored : 86.75 % 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: 2.15 (0.11), residues: 2268 sheet: -1.87 (0.36), residues: 188 loop : -1.63 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 831 HIS 0.003 0.001 HIS B 431 PHE 0.015 0.001 PHE B 175 TYR 0.011 0.001 TYR B 832 ARG 0.002 0.000 ARG D1087 *********************** 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 269 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 227 time to evaluate : 3.411 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: 0.8700 (OUTLIER) cc_final: 0.8421 (p) REVERT: A 196 TYR cc_start: 0.8227 (m-80) cc_final: 0.7910 (m-80) REVERT: A 539 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: B 151 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8422 (p) REVERT: B 539 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: D 151 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8422 (p) REVERT: D 196 TYR cc_start: 0.8211 (m-80) cc_final: 0.7854 (m-80) REVERT: D 539 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: C 151 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8423 (p) REVERT: C 196 TYR cc_start: 0.8212 (m-80) cc_final: 0.7856 (m-80) REVERT: C 539 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7080 (mp0) outliers start: 42 outliers final: 32 residues processed: 254 average time/residue: 0.7640 time to fit residues: 305.6287 Evaluate side-chains 255 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 215 time to evaluate : 3.194 ------------------------------------------------------------------------------- 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 224 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 472 MET 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 352 LEU 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 352 LEU 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 352 LEU Chi-restraints excluded: chain C residue 472 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 2.9990 chunk 322 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 338 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 chunk 269 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 208 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.003 0.046 28920 Z= 0.224 Angle : 0.459 4.247 39284 Z= 0.252 Chirality : 0.036 0.138 4408 Planarity : 0.004 0.064 4808 Dihedral : 7.191 57.970 4884 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.63 % Allowed : 11.45 % Favored : 86.92 % 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: 2.23 (0.11), residues: 2264 sheet: -1.87 (0.37), residues: 188 loop : -1.61 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 831 HIS 0.002 0.000 HIS C 431 PHE 0.013 0.001 PHE B 175 TYR 0.011 0.001 TYR D 832 ARG 0.002 0.000 ARG C1087 ********************** 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 268 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 220 time to evaluate : 3.244 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: A 151 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8258 (p) REVERT: A 196 TYR cc_start: 0.8237 (m-80) cc_final: 0.7886 (m-80) REVERT: A 314 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7890 (t80) REVERT: A 539 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: B 151 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8371 (p) REVERT: B 196 TYR cc_start: 0.8248 (m-80) cc_final: 0.7954 (m-80) REVERT: B 314 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.7892 (t80) REVERT: B 539 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: D 151 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8370 (p) REVERT: D 196 TYR cc_start: 0.8229 (m-80) cc_final: 0.7879 (m-80) REVERT: D 314 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7888 (t80) REVERT: D 539 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: C 151 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8371 (p) REVERT: C 196 TYR cc_start: 0.8230 (m-80) cc_final: 0.7880 (m-80) REVERT: C 314 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7889 (t80) REVERT: C 539 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7080 (mp0) outliers start: 48 outliers final: 32 residues processed: 253 average time/residue: 0.7566 time to fit residues: 302.9534 Evaluate side-chains 259 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 215 time to evaluate : 3.236 ------------------------------------------------------------------------------- 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 211 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 472 MET 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 211 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 352 LEU 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 224 ILE Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 352 LEU 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 314 PHE Chi-restraints excluded: chain C residue 352 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 0.6980 chunk 287 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 248 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 0.0770 chunk 270 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.148055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.093829 restraints weight = 126122.024| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.70 r_work: 0.3088 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 28920 Z= 0.139 Angle : 0.446 12.926 39284 Z= 0.238 Chirality : 0.035 0.139 4408 Planarity : 0.003 0.061 4808 Dihedral : 7.013 59.292 4884 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.49 % Allowed : 11.52 % 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: 1.75 (0.15), residues: 3336 helix: 2.39 (0.11), residues: 2264 sheet: -1.78 (0.37), residues: 188 loop : -1.55 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 831 HIS 0.002 0.000 HIS B 431 PHE 0.012 0.001 PHE A 639 TYR 0.009 0.001 TYR D 832 ARG 0.005 0.000 ARG A1087 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8983.28 seconds wall clock time: 154 minutes 29.52 seconds (9269.52 seconds total)