Starting phenix.real_space_refine (version: dev) on Wed Feb 22 03:59:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/02_2023/8e4l_27891_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/02_2023/8e4l_27891.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/02_2023/8e4l_27891_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/02_2023/8e4l_27891_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/02_2023/8e4l_27891_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/02_2023/8e4l_27891.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/02_2023/8e4l_27891.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/02_2023/8e4l_27891_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/02_2023/8e4l_27891_neut_trim_updated.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.004 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 Process input model Symmetric amino acids flipped Residue "A TYR 981": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 981": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 981": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 981": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 54556 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 13568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 13568 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 21, 'TRANS': 876} Chain breaks: 10 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 281 Chain: "B" Number of atoms: 13568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 13568 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 21, 'TRANS': 876} Chain breaks: 10 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 281 Chain: "C" Number of atoms: 13568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 13568 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 21, 'TRANS': 876} Chain breaks: 10 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 281 Chain: "D" Number of atoms: 13568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 13568 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 21, 'TRANS': 876} Chain breaks: 10 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 281 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {' CA': 1, 'PIO': 1, 'UL9': 1, 'ULO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {' CA': 1, 'PIO': 1, 'UL9': 1, 'ULO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {' CA': 1, 'PIO': 1, 'UL9': 1, 'ULO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {' CA': 1, 'PIO': 1, 'UL9': 1, 'ULO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 18.59, per 1000 atoms: 0.34 Number of scatterers: 54556 At special positions: 0 Unit cell: (152.28, 152.28, 144.72, 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 108 16.00 P 16 15.00 O 4948 8.00 N 4572 7.00 C 18328 6.00 H 26580 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 326 " distance=2.90 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 326 " distance=2.90 Simple disulfide: pdb=" SG CYS C 303 " - pdb=" SG CYS C 326 " distance=2.90 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D 326 " distance=2.90 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 32.33 Conformation dependent library (CDL) restraints added in 3.4 seconds 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6856 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 4 sheets defined 67.9% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.816A pdb=" N ILE A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 201 Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 310 through 322 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 351 through 361 removed outlier: 4.142A pdb=" N LYS A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 371 through 386 removed outlier: 3.841A pdb=" N GLU A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 removed outlier: 4.178A pdb=" N ILE A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 455 through 467 removed outlier: 3.641A pdb=" N ILE A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 503 through 515 Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.626A pdb=" N GLU A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 602 Processing helix chain 'A' and resid 608 through 635 removed outlier: 3.561A pdb=" N GLU A 613 " --> pdb=" O ASN A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 644 Processing helix chain 'A' and resid 656 through 662 Processing helix chain 'A' and resid 666 through 670 Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 692 through 701 removed outlier: 3.611A pdb=" N PHE A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 730 No H-bonds generated for 'chain 'A' and resid 727 through 730' Processing helix chain 'A' and resid 734 through 757 Processing helix chain 'A' and resid 765 through 788 removed outlier: 3.891A pdb=" N LEU A 771 " --> pdb=" O PRO A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 795 No H-bonds generated for 'chain 'A' and resid 792 through 795' Processing helix chain 'A' and resid 797 through 818 Processing helix chain 'A' and resid 822 through 847 removed outlier: 3.573A pdb=" N ARG A 842 " --> pdb=" O ILE A 838 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE A 846 " --> pdb=" O ARG A 842 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 889 Proline residue: A 855 - end of helix removed outlier: 3.988A pdb=" N ILE A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU A 873 " --> pdb=" O PHE A 869 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 913 removed outlier: 3.745A pdb=" N ILE A 899 " --> pdb=" O ARG A 895 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 903 " --> pdb=" O ILE A 899 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR A 905 " --> pdb=" O ARG A 901 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU A 906 " --> pdb=" O SER A 902 " (cutoff:3.500A) Proline residue: A 907 - end of helix removed outlier: 4.535A pdb=" N MET A 911 " --> pdb=" O PRO A 907 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE A 912 " --> pdb=" O TYR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 922 Processing helix chain 'A' and resid 951 through 964 removed outlier: 4.040A pdb=" N ILE A 957 " --> pdb=" O GLU A 953 " (cutoff:3.500A) Proline residue: A 958 - end of helix Processing helix chain 'A' and resid 968 through 988 Processing helix chain 'A' and resid 993 through 1006 removed outlier: 3.915A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS A1006 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1027 removed outlier: 4.400A pdb=" N VAL A1017 " --> pdb=" O PRO A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1103 removed outlier: 4.152A pdb=" N ASN A1074 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER A1075 " --> pdb=" O ALA A1071 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N MET A1078 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG A1079 " --> pdb=" O SER A1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 49 Processing helix chain 'B' and resid 126 through 136 Processing helix chain 'B' and resid 159 through 175 removed outlier: 3.815A pdb=" N ILE B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE B 165 " --> pdb=" O MET B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 201 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 310 through 322 Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 351 through 361 removed outlier: 4.142A pdb=" N LYS B 357 " --> pdb=" O MET B 353 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 371 through 386 removed outlier: 3.841A pdb=" N GLU B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 418 removed outlier: 4.178A pdb=" N ILE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 426 through 436 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 455 through 467 removed outlier: 3.641A pdb=" N ILE B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 484 through 487 No H-bonds generated for 'chain 'B' and resid 484 through 487' Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 503 through 515 Processing helix chain 'B' and resid 519 through 532 Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 574 through 583 removed outlier: 3.626A pdb=" N GLU B 582 " --> pdb=" O LYS B 578 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 602 Processing helix chain 'B' and resid 608 through 635 removed outlier: 3.561A pdb=" N GLU B 613 " --> pdb=" O ASN B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 644 Processing helix chain 'B' and resid 656 through 662 Processing helix chain 'B' and resid 666 through 670 Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 692 through 701 removed outlier: 3.611A pdb=" N PHE B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 730 No H-bonds generated for 'chain 'B' and resid 727 through 730' Processing helix chain 'B' and resid 734 through 757 Processing helix chain 'B' and resid 765 through 788 removed outlier: 3.891A pdb=" N LEU B 771 " --> pdb=" O PRO B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 795 No H-bonds generated for 'chain 'B' and resid 792 through 795' Processing helix chain 'B' and resid 797 through 818 Processing helix chain 'B' and resid 822 through 847 removed outlier: 3.573A pdb=" N ARG B 842 " --> pdb=" O ILE B 838 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE B 846 " --> pdb=" O ARG B 842 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 889 Proline residue: B 855 - end of helix removed outlier: 3.988A pdb=" N ILE B 858 " --> pdb=" O GLY B 854 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE B 872 " --> pdb=" O PHE B 868 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU B 873 " --> pdb=" O PHE B 869 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 884 " --> pdb=" O ALA B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 913 removed outlier: 3.745A pdb=" N ILE B 899 " --> pdb=" O ARG B 895 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 903 " --> pdb=" O ILE B 899 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR B 905 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU B 906 " --> pdb=" O SER B 902 " (cutoff:3.500A) Proline residue: B 907 - end of helix removed outlier: 4.535A pdb=" N MET B 911 " --> pdb=" O PRO B 907 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N PHE B 912 " --> pdb=" O TYR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 922 Processing helix chain 'B' and resid 951 through 964 removed outlier: 4.041A pdb=" N ILE B 957 " --> pdb=" O GLU B 953 " (cutoff:3.500A) Proline residue: B 958 - end of helix Processing helix chain 'B' and resid 968 through 988 Processing helix chain 'B' and resid 993 through 1006 removed outlier: 3.915A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS B1006 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1027 removed outlier: 4.400A pdb=" N VAL B1017 " --> pdb=" O PRO B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1103 removed outlier: 4.152A pdb=" N ASN B1074 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER B1075 " --> pdb=" O ALA B1071 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N MET B1078 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ARG B1079 " --> pdb=" O SER B1075 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 159 through 175 removed outlier: 3.816A pdb=" N ILE C 164 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE C 165 " --> pdb=" O MET C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 201 Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 310 through 322 Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 351 through 361 removed outlier: 4.141A pdb=" N LYS C 357 " --> pdb=" O MET C 353 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 371 through 386 removed outlier: 3.841A pdb=" N GLU C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 418 removed outlier: 4.179A pdb=" N ILE C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER C 409 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 424 Processing helix chain 'C' and resid 426 through 436 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 455 through 467 removed outlier: 3.641A pdb=" N ILE C 467 " --> pdb=" O PHE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 484 through 487 No H-bonds generated for 'chain 'C' and resid 484 through 487' Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 503 through 515 Processing helix chain 'C' and resid 519 through 532 Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 574 through 583 removed outlier: 3.627A pdb=" N GLU C 582 " --> pdb=" O LYS C 578 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 602 Processing helix chain 'C' and resid 608 through 635 removed outlier: 3.561A pdb=" N GLU C 613 " --> pdb=" O ASN C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 644 Processing helix chain 'C' and resid 656 through 662 Processing helix chain 'C' and resid 666 through 670 Processing helix chain 'C' and resid 672 through 683 Processing helix chain 'C' and resid 692 through 701 removed outlier: 3.611A pdb=" N PHE C 700 " --> pdb=" O ILE C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 730 No H-bonds generated for 'chain 'C' and resid 727 through 730' Processing helix chain 'C' and resid 734 through 757 Processing helix chain 'C' and resid 765 through 788 removed outlier: 3.891A pdb=" N LEU C 771 " --> pdb=" O PRO C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 795 No H-bonds generated for 'chain 'C' and resid 792 through 795' Processing helix chain 'C' and resid 797 through 818 Processing helix chain 'C' and resid 822 through 847 removed outlier: 3.573A pdb=" N ARG C 842 " --> pdb=" O ILE C 838 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE C 846 " --> pdb=" O ARG C 842 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE C 847 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 889 Proline residue: C 855 - end of helix removed outlier: 3.988A pdb=" N ILE C 858 " --> pdb=" O GLY C 854 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE C 872 " --> pdb=" O PHE C 868 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU C 873 " --> pdb=" O PHE C 869 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 884 " --> pdb=" O ALA C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 913 removed outlier: 3.744A pdb=" N ILE C 899 " --> pdb=" O ARG C 895 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL C 903 " --> pdb=" O ILE C 899 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR C 905 " --> pdb=" O ARG C 901 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU C 906 " --> pdb=" O SER C 902 " (cutoff:3.500A) Proline residue: C 907 - end of helix removed outlier: 4.535A pdb=" N MET C 911 " --> pdb=" O PRO C 907 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE C 912 " --> pdb=" O TYR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 922 Processing helix chain 'C' and resid 951 through 964 removed outlier: 4.040A pdb=" N ILE C 957 " --> pdb=" O GLU C 953 " (cutoff:3.500A) Proline residue: C 958 - end of helix Processing helix chain 'C' and resid 968 through 988 Processing helix chain 'C' and resid 993 through 1006 removed outlier: 3.916A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS C1006 " --> pdb=" O VAL C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1027 removed outlier: 4.400A pdb=" N VAL C1017 " --> pdb=" O PRO C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1103 removed outlier: 4.152A pdb=" N ASN C1074 " --> pdb=" O LYS C1070 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER C1075 " --> pdb=" O ALA C1071 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N MET C1078 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ARG C1079 " --> pdb=" O SER C1075 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 49 Processing helix chain 'D' and resid 126 through 136 Processing helix chain 'D' and resid 159 through 175 removed outlier: 3.815A pdb=" N ILE D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE D 165 " --> pdb=" O MET D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 201 Processing helix chain 'D' and resid 275 through 286 Processing helix chain 'D' and resid 310 through 322 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 351 through 361 removed outlier: 4.142A pdb=" N LYS D 357 " --> pdb=" O MET D 353 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU D 358 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 368 Processing helix chain 'D' and resid 371 through 386 removed outlier: 3.840A pdb=" N GLU D 375 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 418 removed outlier: 4.178A pdb=" N ILE D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER D 409 " --> pdb=" O SER D 405 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 415 " --> pdb=" O ALA D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 424 Processing helix chain 'D' and resid 426 through 436 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 455 through 467 removed outlier: 3.642A pdb=" N ILE D 467 " --> pdb=" O PHE D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 480 Processing helix chain 'D' and resid 484 through 487 No H-bonds generated for 'chain 'D' and resid 484 through 487' Processing helix chain 'D' and resid 490 through 499 Processing helix chain 'D' and resid 503 through 515 Processing helix chain 'D' and resid 519 through 532 Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 574 through 583 removed outlier: 3.626A pdb=" N GLU D 582 " --> pdb=" O LYS D 578 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN D 583 " --> pdb=" O VAL D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 602 Processing helix chain 'D' and resid 608 through 635 removed outlier: 3.560A pdb=" N GLU D 613 " --> pdb=" O ASN D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 644 Processing helix chain 'D' and resid 656 through 662 Processing helix chain 'D' and resid 666 through 670 Processing helix chain 'D' and resid 672 through 683 Processing helix chain 'D' and resid 692 through 701 removed outlier: 3.611A pdb=" N PHE D 700 " --> pdb=" O ILE D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 730 No H-bonds generated for 'chain 'D' and resid 727 through 730' Processing helix chain 'D' and resid 734 through 757 Processing helix chain 'D' and resid 765 through 788 removed outlier: 3.891A pdb=" N LEU D 771 " --> pdb=" O PRO D 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 795 No H-bonds generated for 'chain 'D' and resid 792 through 795' Processing helix chain 'D' and resid 797 through 818 Processing helix chain 'D' and resid 822 through 847 removed outlier: 3.573A pdb=" N ARG D 842 " --> pdb=" O ILE D 838 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE D 846 " --> pdb=" O ARG D 842 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE D 847 " --> pdb=" O LEU D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 889 Proline residue: D 855 - end of helix removed outlier: 3.988A pdb=" N ILE D 858 " --> pdb=" O GLY D 854 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE D 872 " --> pdb=" O PHE D 868 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU D 873 " --> pdb=" O PHE D 869 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 884 " --> pdb=" O ALA D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 913 removed outlier: 3.744A pdb=" N ILE D 899 " --> pdb=" O ARG D 895 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL D 903 " --> pdb=" O ILE D 899 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR D 905 " --> pdb=" O ARG D 901 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU D 906 " --> pdb=" O SER D 902 " (cutoff:3.500A) Proline residue: D 907 - end of helix removed outlier: 4.535A pdb=" N MET D 911 " --> pdb=" O PRO D 907 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE D 912 " --> pdb=" O TYR D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 922 Processing helix chain 'D' and resid 951 through 964 removed outlier: 4.040A pdb=" N ILE D 957 " --> pdb=" O GLU D 953 " (cutoff:3.500A) Proline residue: D 958 - end of helix Processing helix chain 'D' and resid 968 through 988 Processing helix chain 'D' and resid 993 through 1006 removed outlier: 3.915A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR D1005 " --> pdb=" O LEU D1001 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS D1006 " --> pdb=" O VAL D1002 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1027 removed outlier: 4.400A pdb=" N VAL D1017 " --> pdb=" O PRO D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1051 through 1103 removed outlier: 4.153A pdb=" N ASN D1074 " --> pdb=" O LYS D1070 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER D1075 " --> pdb=" O ALA D1071 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N MET D1078 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ARG D1079 " --> pdb=" O SER D1075 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.593A pdb=" N HIS A 259 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE A 146 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 302 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA A 305 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 327 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.593A pdb=" N HIS B 259 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE B 146 " --> pdb=" O PRO B 300 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 302 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA B 305 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL B 327 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.593A pdb=" N HIS C 259 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE C 146 " --> pdb=" O PRO C 300 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 302 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ALA C 305 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL C 327 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 116 through 120 removed outlier: 3.593A pdb=" N HIS D 259 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE D 146 " --> pdb=" O PRO D 300 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL D 302 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ALA D 305 " --> pdb=" O PRO D 325 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL D 327 " --> pdb=" O ALA D 305 " (cutoff:3.500A) 1624 hydrogen bonds defined for protein. 4728 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: 16.32 Time building geometry restraints manager: 34.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.03: 26540 1.03 - 1.24: 2867 1.24 - 1.45: 9624 1.45 - 1.65: 15953 1.65 - 1.86: 192 Bond restraints: 55176 Sorted by residual: bond pdb=" C02 UL9 C1202 " pdb=" C03 UL9 C1202 " ideal model delta sigma weight residual 1.527 1.707 -0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" C02 UL9 D1202 " pdb=" C03 UL9 D1202 " ideal model delta sigma weight residual 1.527 1.707 -0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" C02 UL9 A1202 " pdb=" C03 UL9 A1202 " ideal model delta sigma weight residual 1.527 1.706 -0.179 2.00e-02 2.50e+03 8.03e+01 bond pdb=" C02 UL9 B1202 " pdb=" C03 UL9 B1202 " ideal model delta sigma weight residual 1.527 1.706 -0.179 2.00e-02 2.50e+03 7.99e+01 bond pdb=" C03 UL9 B1202 " pdb=" N04 UL9 B1202 " ideal model delta sigma weight residual 1.452 1.609 -0.157 2.00e-02 2.50e+03 6.20e+01 ... (remaining 55171 not shown) Histogram of bond angle deviations from ideal: 100.10 - 116.06: 68916 116.06 - 132.02: 30188 132.02 - 147.98: 88 147.98 - 163.94: 0 163.94 - 179.89: 4 Bond angle restraints: 99196 Sorted by residual: angle pdb=" N04 UL9 B1202 " pdb=" C05 UL9 B1202 " pdb=" S06 UL9 B1202 " ideal model delta sigma weight residual 107.78 179.89 -72.11 1.00e+00 1.00e+00 5.20e+03 angle pdb=" N04 UL9 A1202 " pdb=" C05 UL9 A1202 " pdb=" S06 UL9 A1202 " ideal model delta sigma weight residual 107.78 179.88 -72.10 1.00e+00 1.00e+00 5.20e+03 angle pdb=" N04 UL9 D1202 " pdb=" C05 UL9 D1202 " pdb=" S06 UL9 D1202 " ideal model delta sigma weight residual 107.78 179.85 -72.07 1.00e+00 1.00e+00 5.19e+03 angle pdb=" N04 UL9 C1202 " pdb=" C05 UL9 C1202 " pdb=" S06 UL9 C1202 " ideal model delta sigma weight residual 107.78 179.83 -72.05 1.00e+00 1.00e+00 5.19e+03 angle pdb=" N MET C 859 " pdb=" CA MET C 859 " pdb=" C MET C 859 " ideal model delta sigma weight residual 111.36 105.54 5.82 1.09e+00 8.42e-01 2.85e+01 ... (remaining 99191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 20492 14.03 - 28.05: 1576 28.05 - 42.08: 325 42.08 - 56.10: 115 56.10 - 70.13: 40 Dihedral angle restraints: 22548 sinusoidal: 9648 harmonic: 12900 Sorted by residual: dihedral pdb=" CB CYS C 303 " pdb=" SG CYS C 303 " pdb=" SG CYS C 326 " pdb=" CB CYS C 326 " ideal model delta sinusoidal sigma weight residual -86.00 -19.91 -66.09 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CB CYS D 303 " pdb=" SG CYS D 303 " pdb=" SG CYS D 326 " pdb=" CB CYS D 326 " ideal model delta sinusoidal sigma weight residual -86.00 -19.91 -66.09 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CB CYS A 303 " pdb=" SG CYS A 303 " pdb=" SG CYS A 326 " pdb=" CB CYS A 326 " ideal model delta sinusoidal sigma weight residual -86.00 -19.91 -66.09 1 1.00e+01 1.00e-02 5.71e+01 ... (remaining 22545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3346 0.036 - 0.071: 811 0.071 - 0.107: 264 0.107 - 0.143: 63 0.143 - 0.179: 12 Chirality restraints: 4496 Sorted by residual: chirality pdb=" CA VAL B 972 " pdb=" N VAL B 972 " pdb=" C VAL B 972 " pdb=" CB VAL B 972 " both_signs ideal model delta sigma weight residual False 2.44 2.26 0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA VAL A 972 " pdb=" N VAL A 972 " pdb=" C VAL A 972 " pdb=" CB VAL A 972 " both_signs ideal model delta sigma weight residual False 2.44 2.26 0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CA VAL C 972 " pdb=" N VAL C 972 " pdb=" C VAL C 972 " pdb=" CB VAL C 972 " both_signs ideal model delta sigma weight residual False 2.44 2.26 0.18 2.00e-01 2.50e+01 7.96e-01 ... (remaining 4493 not shown) Planarity restraints: 8252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 PIO C1204 " -0.455 2.00e-02 2.50e+03 4.78e-01 6.85e+03 pdb=" C2 PIO C1204 " -0.231 2.00e-02 2.50e+03 pdb=" C3 PIO C1204 " -0.585 2.00e-02 2.50e+03 pdb=" C4 PIO C1204 " 0.214 2.00e-02 2.50e+03 pdb=" C5 PIO C1204 " -0.146 2.00e-02 2.50e+03 pdb=" C6 PIO C1204 " 0.101 2.00e-02 2.50e+03 pdb=" O1 PIO C1204 " 0.192 2.00e-02 2.50e+03 pdb=" O2 PIO C1204 " 1.126 2.00e-02 2.50e+03 pdb=" O3 PIO C1204 " -0.278 2.00e-02 2.50e+03 pdb=" O4 PIO C1204 " -0.074 2.00e-02 2.50e+03 pdb=" O5 PIO C1204 " 0.644 2.00e-02 2.50e+03 pdb=" O6 PIO C1204 " -0.507 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PIO B1204 " 0.456 2.00e-02 2.50e+03 4.78e-01 6.85e+03 pdb=" C2 PIO B1204 " 0.231 2.00e-02 2.50e+03 pdb=" C3 PIO B1204 " 0.585 2.00e-02 2.50e+03 pdb=" C4 PIO B1204 " -0.214 2.00e-02 2.50e+03 pdb=" C5 PIO B1204 " 0.146 2.00e-02 2.50e+03 pdb=" C6 PIO B1204 " -0.102 2.00e-02 2.50e+03 pdb=" O1 PIO B1204 " -0.192 2.00e-02 2.50e+03 pdb=" O2 PIO B1204 " -1.125 2.00e-02 2.50e+03 pdb=" O3 PIO B1204 " 0.278 2.00e-02 2.50e+03 pdb=" O4 PIO B1204 " 0.075 2.00e-02 2.50e+03 pdb=" O5 PIO B1204 " -0.644 2.00e-02 2.50e+03 pdb=" O6 PIO B1204 " 0.507 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PIO D1204 " -0.455 2.00e-02 2.50e+03 4.78e-01 6.85e+03 pdb=" C2 PIO D1204 " -0.231 2.00e-02 2.50e+03 pdb=" C3 PIO D1204 " -0.585 2.00e-02 2.50e+03 pdb=" C4 PIO D1204 " 0.214 2.00e-02 2.50e+03 pdb=" C5 PIO D1204 " -0.147 2.00e-02 2.50e+03 pdb=" C6 PIO D1204 " 0.102 2.00e-02 2.50e+03 pdb=" O1 PIO D1204 " 0.192 2.00e-02 2.50e+03 pdb=" O2 PIO D1204 " 1.125 2.00e-02 2.50e+03 pdb=" O3 PIO D1204 " -0.278 2.00e-02 2.50e+03 pdb=" O4 PIO D1204 " -0.074 2.00e-02 2.50e+03 pdb=" O5 PIO D1204 " 0.644 2.00e-02 2.50e+03 pdb=" O6 PIO D1204 " -0.507 2.00e-02 2.50e+03 ... (remaining 8249 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.12: 1231 2.12 - 2.74: 95933 2.74 - 3.36: 152995 3.36 - 3.98: 180695 3.98 - 4.60: 291946 Nonbonded interactions: 722800 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 605 " pdb=" O41 PIO D1204 " model vdw 1.506 1.850 nonbonded pdb=" HZ1 LYS D 605 " pdb=" O41 PIO C1204 " model vdw 1.586 1.850 nonbonded pdb=" O LEU C 120 " pdb=" H ASP C 264 " model vdw 1.589 1.850 nonbonded pdb=" O LEU A 120 " pdb=" H ASP A 264 " model vdw 1.589 1.850 nonbonded pdb=" O LEU D 120 " pdb=" H ASP D 264 " model vdw 1.589 1.850 ... (remaining 722795 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 16 5.49 5 S 108 5.16 5 C 18328 2.51 5 N 4572 2.21 5 O 4948 1.98 5 H 26580 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.890 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: 0.610 Extract box with map and model: 6.880 Check model and map are aligned: 0.600 Process input model: 121.510 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.370 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.180 28596 Z= 0.264 Angle : 0.905 72.115 38896 Z= 0.791 Chirality : 0.038 0.179 4496 Planarity : 0.014 0.478 4788 Dihedral : 11.256 70.129 9872 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 0.00 % 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: 2.40 (0.14), residues: 3504 helix: 2.55 (0.11), residues: 2444 sheet: -0.11 (0.40), residues: 196 loop : -0.91 (0.19), residues: 864 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 586 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 586 time to evaluate : 3.274 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 586 average time/residue: 0.7222 time to fit residues: 658.5837 Evaluate side-chains 309 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 3.328 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 20.0000 chunk 269 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 279 optimal weight: 30.0000 chunk 107 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 323 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN A 997 GLN B 389 HIS ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 861 GLN B 973 ASN C 389 HIS ** C 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 ASN C 861 GLN C 973 ASN ** D 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 ASN D 861 GLN D 997 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 28596 Z= 0.371 Angle : 0.742 14.432 38896 Z= 0.352 Chirality : 0.037 0.147 4496 Planarity : 0.003 0.028 4788 Dihedral : 7.739 95.205 4068 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 1.31 % 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: 2.01 (0.14), residues: 3504 helix: 2.30 (0.10), residues: 2424 sheet: -0.42 (0.38), residues: 196 loop : -1.03 (0.19), residues: 884 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 360 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 324 time to evaluate : 3.303 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 22 residues processed: 349 average time/residue: 0.7249 time to fit residues: 404.3158 Evaluate side-chains 311 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 289 time to evaluate : 3.317 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4592 time to fit residues: 23.4636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 269 optimal weight: 9.9990 chunk 220 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 323 optimal weight: 6.9990 chunk 349 optimal weight: 7.9990 chunk 288 optimal weight: 7.9990 chunk 321 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 259 optimal weight: 3.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 ASN A 671 GLN ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN ** C 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 GLN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 28596 Z= 0.300 Angle : 0.689 13.234 38896 Z= 0.324 Chirality : 0.037 0.171 4496 Planarity : 0.003 0.031 4788 Dihedral : 7.268 72.227 4068 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.14), residues: 3504 helix: 2.21 (0.10), residues: 2428 sheet: -0.49 (0.38), residues: 196 loop : -1.10 (0.19), residues: 880 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 315 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 296 time to evaluate : 3.337 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 outliers start: 19 outliers final: 3 residues processed: 311 average time/residue: 0.6636 time to fit residues: 335.3523 Evaluate side-chains 267 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 264 time to evaluate : 3.342 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5425 time to fit residues: 7.0300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 3.9990 chunk 243 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 325 optimal weight: 4.9990 chunk 344 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 chunk 308 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 459 GLN B 255 ASN B 459 GLN C 255 ASN C 459 GLN C 987 GLN D 255 ASN D 459 GLN ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 28596 Z= 0.253 Angle : 0.670 12.731 38896 Z= 0.311 Chirality : 0.037 0.256 4496 Planarity : 0.003 0.028 4788 Dihedral : 7.050 57.323 4068 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 1.20 % 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: 1.95 (0.14), residues: 3504 helix: 2.29 (0.10), residues: 2440 sheet: -0.63 (0.36), residues: 196 loop : -1.22 (0.19), residues: 868 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 322 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 289 time to evaluate : 3.356 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: symmetry clash outliers start: 33 outliers final: 17 residues processed: 312 average time/residue: 0.6677 time to fit residues: 339.8573 Evaluate side-chains 281 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 264 time to evaluate : 3.348 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4966 time to fit residues: 19.4284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 20.0000 chunk 195 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 256 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 293 optimal weight: 8.9990 chunk 237 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 308 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 GLN ** D 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN D 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 28596 Z= 0.195 Angle : 0.657 12.491 38896 Z= 0.300 Chirality : 0.036 0.277 4496 Planarity : 0.003 0.023 4788 Dihedral : 6.936 57.459 4068 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.65 % 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: 2.06 (0.14), residues: 3504 helix: 2.40 (0.11), residues: 2448 sheet: -0.93 (0.36), residues: 196 loop : -1.22 (0.19), residues: 860 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 305 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 287 time to evaluate : 3.840 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: symmetry clash outliers start: 18 outliers final: 4 residues processed: 298 average time/residue: 0.6872 time to fit residues: 331.8119 Evaluate side-chains 277 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 273 time to evaluate : 3.345 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4771 time to fit residues: 7.7113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 10.0000 chunk 309 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 344 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 180 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 28596 Z= 0.166 Angle : 0.645 12.184 38896 Z= 0.289 Chirality : 0.035 0.236 4496 Planarity : 0.002 0.023 4788 Dihedral : 6.866 57.299 4068 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.54 % 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: 2.25 (0.15), residues: 3504 helix: 2.53 (0.11), residues: 2428 sheet: -0.88 (0.37), residues: 192 loop : -0.98 (0.20), residues: 884 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 313 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 298 time to evaluate : 3.322 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 309 average time/residue: 0.6635 time to fit residues: 335.1588 Evaluate side-chains 277 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 272 time to evaluate : 3.361 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6305 time to fit residues: 9.7203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 251 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 289 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 343 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 28596 Z= 0.396 Angle : 0.724 13.353 38896 Z= 0.345 Chirality : 0.038 0.269 4496 Planarity : 0.003 0.024 4788 Dihedral : 7.128 57.264 4068 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 1.02 % 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: 1.58 (0.14), residues: 3504 helix: 2.05 (0.10), residues: 2448 sheet: -1.23 (0.36), residues: 196 loop : -1.36 (0.19), residues: 860 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 301 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 273 time to evaluate : 3.419 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 outliers start: 28 outliers final: 17 residues processed: 292 average time/residue: 0.6538 time to fit residues: 315.7864 Evaluate side-chains 280 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 263 time to evaluate : 4.112 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4821 time to fit residues: 19.7221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 233 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 269 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 GLN D 459 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 28596 Z= 0.214 Angle : 0.669 12.513 38896 Z= 0.305 Chirality : 0.036 0.233 4496 Planarity : 0.002 0.026 4788 Dihedral : 7.044 57.466 4068 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.29 % 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: 1.88 (0.14), residues: 3504 helix: 2.28 (0.10), residues: 2448 sheet: -1.05 (0.37), residues: 192 loop : -1.30 (0.19), residues: 864 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 275 time to evaluate : 3.506 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: symmetry clash outliers start: 8 outliers final: 4 residues processed: 279 average time/residue: 0.6831 time to fit residues: 310.0064 Evaluate side-chains 268 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 264 time to evaluate : 3.291 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4490 time to fit residues: 7.5634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 3.9990 chunk 328 optimal weight: 9.9990 chunk 299 optimal weight: 7.9990 chunk 319 optimal weight: 0.9980 chunk 192 optimal weight: 20.0000 chunk 139 optimal weight: 0.9980 chunk 251 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 288 optimal weight: 7.9990 chunk 302 optimal weight: 2.9990 chunk 318 optimal weight: 0.6980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 GLN A 676 ASN B 459 GLN C 676 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 28596 Z= 0.171 Angle : 0.655 12.181 38896 Z= 0.294 Chirality : 0.036 0.204 4496 Planarity : 0.002 0.022 4788 Dihedral : 6.975 56.782 4068 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 0.11 % 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: 2.10 (0.15), residues: 3504 helix: 2.45 (0.11), residues: 2428 sheet: -1.04 (0.37), residues: 192 loop : -1.14 (0.19), residues: 884 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 275 time to evaluate : 3.354 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: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 276 average time/residue: 0.7032 time to fit residues: 314.4314 Evaluate side-chains 267 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 265 time to evaluate : 3.342 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5222 time to fit residues: 6.0514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 4.9990 chunk 338 optimal weight: 5.9990 chunk 206 optimal weight: 0.0270 chunk 160 optimal weight: 6.9990 chunk 235 optimal weight: 3.9990 chunk 354 optimal weight: 20.0000 chunk 326 optimal weight: 8.9990 chunk 282 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 218 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 overall best weight: 2.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 ASN C 676 ASN D 671 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 28596 Z= 0.199 Angle : 0.657 12.333 38896 Z= 0.297 Chirality : 0.036 0.185 4496 Planarity : 0.002 0.022 4788 Dihedral : 6.956 56.163 4068 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.14), residues: 3504 helix: 2.45 (0.11), residues: 2428 sheet: -1.07 (0.37), residues: 192 loop : -1.18 (0.19), residues: 884 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 275 time to evaluate : 3.443 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: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 276 average time/residue: 0.6967 time to fit residues: 313.1533 Evaluate side-chains 270 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 3.302 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4577 time to fit residues: 5.0247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 1.9990 chunk 300 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 260 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 282 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 290 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 ASN B 676 ASN C 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.120698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.088293 restraints weight = 201842.994| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.45 r_work: 0.3213 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 28596 Z= 0.150 Angle : 0.645 11.981 38896 Z= 0.287 Chirality : 0.035 0.171 4496 Planarity : 0.002 0.022 4788 Dihedral : 6.923 56.934 4068 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 0.04 % 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: 2.26 (0.15), residues: 3504 helix: 2.58 (0.11), residues: 2428 sheet: -1.00 (0.38), residues: 192 loop : -1.12 (0.19), residues: 884 =============================================================================== Job complete usr+sys time: 8373.79 seconds wall clock time: 146 minutes 25.11 seconds (8785.11 seconds total)