Starting phenix.real_space_refine on Thu Mar 21 10:09:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/03_2024/7wk9_32563.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/03_2024/7wk9_32563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/03_2024/7wk9_32563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/03_2024/7wk9_32563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/03_2024/7wk9_32563.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/03_2024/7wk9_32563.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 18997 2.51 5 N 4964 2.21 5 O 5651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29745 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8165 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 54, 'TRANS': 987} Chain breaks: 7 Chain: "C" Number of atoms: 8239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8239 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 54, 'TRANS': 996} Chain breaks: 7 Chain: "c" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "d" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 8239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8239 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 54, 'TRANS': 996} Chain breaks: 7 Chain: "a" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "b" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 15.46, per 1000 atoms: 0.52 Number of scatterers: 29745 At special positions: 0 Unit cell: (185.81, 137.718, 196.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 133 16.00 O 5651 8.00 N 4964 7.00 C 18997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 96 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 92 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 96 " distance=2.03 Simple disulfide: pdb=" SG CYS a 147 " - pdb=" SG CYS a 202 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 92 " distance=2.03 Simple disulfide: pdb=" SG CYS b 138 " - pdb=" SG CYS b 198 " distance=2.03 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: 10.99 Conformation dependent library (CDL) restraints added in 5.5 seconds 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7136 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 67 sheets defined 18.3% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.736A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.628A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.856A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.622A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.827A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 4.026A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 removed outlier: 3.503A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 909 removed outlier: 3.719A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.735A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 919' Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.613A pdb=" N ALA A 924 " --> pdb=" O GLN A 920 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 960 removed outlier: 3.710A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 965 removed outlier: 3.745A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.553A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 977 through 982' Processing helix chain 'A' and resid 988 through 1031 removed outlier: 3.993A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.673A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.378A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.694A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.958A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.790A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.892A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 746 through 752' Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.913A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.511A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.879A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.601A pdb=" N ALA C 876 " --> pdb=" O GLN C 872 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 906 removed outlier: 3.913A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.814A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.609A pdb=" N ALA C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 963 removed outlier: 3.820A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.571A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.871A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.812A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 56 No H-bonds generated for 'chain 'd' and resid 54 through 56' Processing helix chain 'd' and resid 83 through 87 removed outlier: 4.106A pdb=" N ALA d 87 " --> pdb=" O GLU d 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.617A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.262A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 410' Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.527A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.813A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.763A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.932A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 824 removed outlier: 3.860A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.814A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.601A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.676A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.661A pdb=" N ALA B 924 " --> pdb=" O GLN B 920 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 963 removed outlier: 3.799A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.660A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1032 removed outlier: 3.644A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET B1029 " --> pdb=" O ALA B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.901A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 32 removed outlier: 3.581A pdb=" N ARG a 31 " --> pdb=" O SER a 28 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE a 32 " --> pdb=" O PHE a 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 28 through 32' Processing helix chain 'a' and resid 87 through 91 removed outlier: 3.879A pdb=" N SER a 91 " --> pdb=" O SER a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 198 removed outlier: 4.014A pdb=" N SER a 197 " --> pdb=" O SER a 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 87 removed outlier: 4.245A pdb=" N ALA b 87 " --> pdb=" O GLU b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 132 removed outlier: 3.560A pdb=" N LEU b 129 " --> pdb=" O SER b 125 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER b 131 " --> pdb=" O GLU b 127 " (cutoff:3.500A) Processing helix chain 'b' and resid 187 through 192 removed outlier: 3.892A pdb=" N ARG b 192 " --> pdb=" O ASP b 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.524A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.780A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.525A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.534A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 removed outlier: 5.853A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.507A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 511 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.590A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 8.209A pdb=" N ASN A 450 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N ARG A 493 " --> pdb=" O ASN A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.075A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.765A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.456A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.634A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A1060 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.613A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.923A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.506A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 48 through 52 removed outlier: 3.745A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.633A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.633A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.005A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.684A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.566A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.514A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.952A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.720A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AD4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.721A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.663A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.972A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'c' and resid 9 through 11 removed outlier: 3.757A pdb=" N TYR c 95 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL c 37 " --> pdb=" O TYR c 95 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N MET c 34 " --> pdb=" O MET c 50 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N MET c 50 " --> pdb=" O MET c 34 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP c 36 " --> pdb=" O ILE c 48 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG c 40 " --> pdb=" O GLY c 44 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY c 44 " --> pdb=" O ARG c 40 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU c 57 " --> pdb=" O HIS c 52 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 9 through 11 removed outlier: 6.667A pdb=" N CYS c 96 " --> pdb=" O TRP c 110 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TRP c 110 " --> pdb=" O CYS c 96 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG c 98 " --> pdb=" O ALA c 108 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP c 106 " --> pdb=" O ASP c 100 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'c' and resid 17 through 23 removed outlier: 3.827A pdb=" N MET c 81 " --> pdb=" O LEU c 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR c 71 " --> pdb=" O TYR c 80 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 4 through 7 removed outlier: 3.812A pdb=" N SER d 7 " --> pdb=" O SER d 22 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER d 22 " --> pdb=" O SER d 7 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS d 23 " --> pdb=" O PHE d 75 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE d 75 " --> pdb=" O CYS d 23 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP d 74 " --> pdb=" O SER d 71 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER d 71 " --> pdb=" O ASP d 74 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 10 through 14 removed outlier: 6.628A pdb=" N LEU d 11 " --> pdb=" O GLU d 109 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS d 111 " --> pdb=" O LEU d 11 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL d 13 " --> pdb=" O LYS d 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'd' and resid 52 through 53 Processing sheet with id=AE6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.595A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.629A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.762A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 244 through 245 Processing sheet with id=AF1, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.393A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.882A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.879A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.678A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.749A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AF8, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.681A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AG1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.841A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AG3, first strand: chain 'a' and resid 9 through 12 removed outlier: 3.709A pdb=" N VAL a 12 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA a 92 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS a 99 " --> pdb=" O TRP a 33 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TRP a 33 " --> pdb=" O LYS a 99 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N MET a 34 " --> pdb=" O MET a 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TRP a 36 " --> pdb=" O ILE a 48 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG a 40 " --> pdb=" O GLY a 44 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 9 through 12 removed outlier: 3.709A pdb=" N VAL a 12 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA a 92 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG a 98 " --> pdb=" O TYR a 109 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR a 109 " --> pdb=" O ARG a 98 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 17 through 23 removed outlier: 3.757A pdb=" N THR a 71 " --> pdb=" O TYR a 80 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 127 through 131 removed outlier: 6.402A pdb=" N TYR a 182 " --> pdb=" O GLY a 151 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER a 187 " --> pdb=" O HIS a 171 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'a' and resid 127 through 131 removed outlier: 6.402A pdb=" N TYR a 182 " --> pdb=" O GLY a 151 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a' and resid 158 through 161 removed outlier: 3.539A pdb=" N THR a 211 " --> pdb=" O HIS a 206 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 5 through 7 removed outlier: 3.701A pdb=" N SER b 7 " --> pdb=" O SER b 22 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER b 22 " --> pdb=" O SER b 7 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS b 23 " --> pdb=" O PHE b 75 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE b 75 " --> pdb=" O CYS b 23 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP b 74 " --> pdb=" O SER b 71 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 10 through 13 removed outlier: 6.256A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP b 39 " --> pdb=" O LEU b 51 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN b 41 " --> pdb=" O LYS b 49 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 10 through 13 removed outlier: 6.256A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HIS b 94 " --> pdb=" O ALA b 101 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA b 101 " --> pdb=" O HIS b 94 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 118 through 122 removed outlier: 3.540A pdb=" N VAL b 137 " --> pdb=" O PHE b 122 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR b 177 " --> pdb=" O ASN b 142 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 157 through 158 removed outlier: 3.829A pdb=" N TYR b 196 " --> pdb=" O PHE b 213 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE b 213 " --> pdb=" O TYR b 196 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA b 200 " --> pdb=" O ILE b 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE b 209 " --> pdb=" O ALA b 200 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2418 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: 14.45 Time building geometry restraints manager: 11.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9136 1.34 - 1.46: 6545 1.46 - 1.58: 14606 1.58 - 1.70: 0 1.70 - 1.82: 170 Bond restraints: 30457 Sorted by residual: bond pdb=" N LEU C 24 " pdb=" CA LEU C 24 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.87e+01 bond pdb=" N LEU B 24 " pdb=" CA LEU B 24 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.85e+01 bond pdb=" C GLY B 526 " pdb=" N PRO B 527 " ideal model delta sigma weight residual 1.334 1.433 -0.099 2.34e-02 1.83e+03 1.78e+01 bond pdb=" N GLN C 271 " pdb=" CA GLN C 271 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.43e+01 bond pdb=" N LEU A 24 " pdb=" CA LEU A 24 " ideal model delta sigma weight residual 1.452 1.489 -0.036 1.11e-02 8.12e+03 1.07e+01 ... (remaining 30452 not shown) Histogram of bond angle deviations from ideal: 99.92 - 107.07: 1019 107.07 - 114.22: 17020 114.22 - 121.37: 15000 121.37 - 128.52: 8208 128.52 - 135.67: 186 Bond angle restraints: 41433 Sorted by residual: angle pdb=" C ASN B 122 " pdb=" N ALA B 123 " pdb=" CA ALA B 123 " ideal model delta sigma weight residual 121.54 132.51 -10.97 1.91e+00 2.74e-01 3.30e+01 angle pdb=" C GLY B 639 " pdb=" N SER B 640 " pdb=" CA SER B 640 " ideal model delta sigma weight residual 121.54 132.00 -10.46 1.91e+00 2.74e-01 3.00e+01 angle pdb=" C GLY C 639 " pdb=" N SER C 640 " pdb=" CA SER C 640 " ideal model delta sigma weight residual 121.54 131.61 -10.07 1.91e+00 2.74e-01 2.78e+01 angle pdb=" C CYS B 525 " pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sigma weight residual 117.23 110.67 6.56 1.36e+00 5.41e-01 2.33e+01 angle pdb=" N GLY A 504 " pdb=" CA GLY A 504 " pdb=" C GLY A 504 " ideal model delta sigma weight residual 113.37 119.37 -6.00 1.34e+00 5.57e-01 2.00e+01 ... (remaining 41428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 17711 17.42 - 34.84: 341 34.84 - 52.27: 110 52.27 - 69.69: 15 69.69 - 87.11: 2 Dihedral angle restraints: 18179 sinusoidal: 7093 harmonic: 11086 Sorted by residual: dihedral pdb=" CA LYS B 795 " pdb=" C LYS B 795 " pdb=" N TYR B 796 " pdb=" CA TYR B 796 " ideal model delta harmonic sigma weight residual 180.00 155.50 24.50 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA TYR a 101 " pdb=" C TYR a 101 " pdb=" N ASP a 102 " pdb=" CA ASP a 102 " ideal model delta harmonic sigma weight residual 180.00 156.26 23.74 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ARG C 634 " pdb=" C ARG C 634 " pdb=" N VAL C 635 " pdb=" CA VAL C 635 " ideal model delta harmonic sigma weight residual -180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 18176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3570 0.056 - 0.112: 863 0.112 - 0.169: 199 0.169 - 0.225: 31 0.225 - 0.281: 8 Chirality restraints: 4671 Sorted by residual: chirality pdb=" CB ILE C 312 " pdb=" CA ILE C 312 " pdb=" CG1 ILE C 312 " pdb=" CG2 ILE C 312 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE B 312 " pdb=" CA ILE B 312 " pdb=" CG1 ILE B 312 " pdb=" CG2 ILE B 312 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE b 121 " pdb=" CA ILE b 121 " pdb=" CG1 ILE b 121 " pdb=" CG2 ILE b 121 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 4668 not shown) Planarity restraints: 5342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.054 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 295 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 445 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.09e+00 pdb=" C VAL A 445 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL A 445 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 446 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.047 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO B 987 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.040 5.00e-02 4.00e+02 ... (remaining 5339 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 9257 2.85 - 3.37: 22275 3.37 - 3.88: 47980 3.88 - 4.39: 50056 4.39 - 4.90: 90211 Nonbonded interactions: 219779 Sorted by model distance: nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.342 2.440 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.345 2.440 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.351 2.440 nonbonded pdb=" O ALA A 879 " pdb=" OG1 THR A 883 " model vdw 2.351 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.352 2.440 ... (remaining 219774 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' and (resid 14 through 631 or resid 641 through 1147)) selection = (chain 'C' and (resid 14 through 631 or resid 641 through 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 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: 0.030 Extract box with map and model: 12.000 Check model and map are aligned: 0.460 Set scattering table: 0.260 Process input model: 81.700 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 30457 Z= 0.301 Angle : 0.785 10.974 41433 Z= 0.459 Chirality : 0.053 0.281 4671 Planarity : 0.006 0.082 5342 Dihedral : 8.279 87.110 10914 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.89 % Favored : 95.95 % Rotamer: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -2.70 (0.11), residues: 3749 helix: -4.92 (0.05), residues: 574 sheet: -0.20 (0.16), residues: 750 loop : -1.57 (0.10), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 33 HIS 0.012 0.001 HIS B 954 PHE 0.026 0.003 PHE B 490 TYR 0.032 0.002 TYR d 53 ARG 0.006 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 930 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.5319 (mtt-85) cc_final: 0.4502 (ttp80) REVERT: A 95 ILE cc_start: 0.7552 (mt) cc_final: 0.7285 (tp) REVERT: A 196 ASN cc_start: 0.7666 (t0) cc_final: 0.7361 (t0) REVERT: A 270 LEU cc_start: 0.7719 (mp) cc_final: 0.6488 (mp) REVERT: A 309 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7026 (mt-10) REVERT: A 654 GLU cc_start: 0.7186 (tt0) cc_final: 0.6947 (tt0) REVERT: A 780 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7625 (mt-10) REVERT: A 804 GLN cc_start: 0.7882 (mt0) cc_final: 0.7605 (mt0) REVERT: A 868 GLU cc_start: 0.8262 (tt0) cc_final: 0.8035 (tt0) REVERT: A 870 ILE cc_start: 0.7420 (mt) cc_final: 0.7212 (mt) REVERT: A 883 THR cc_start: 0.8317 (p) cc_final: 0.7402 (m) REVERT: A 969 LYS cc_start: 0.8296 (mttt) cc_final: 0.7549 (mmmt) REVERT: A 979 ASP cc_start: 0.7340 (m-30) cc_final: 0.7006 (t0) REVERT: A 984 LEU cc_start: 0.7935 (mt) cc_final: 0.7637 (mm) REVERT: A 985 ASP cc_start: 0.7778 (m-30) cc_final: 0.7415 (m-30) REVERT: C 33 THR cc_start: 0.7954 (p) cc_final: 0.7622 (p) REVERT: C 36 VAL cc_start: 0.8566 (t) cc_final: 0.8338 (p) REVERT: C 81 ASN cc_start: 0.8323 (t0) cc_final: 0.8061 (m-40) REVERT: C 92 PHE cc_start: 0.6637 (t80) cc_final: 0.6436 (t80) REVERT: C 201 PHE cc_start: 0.8229 (t80) cc_final: 0.7996 (t80) REVERT: C 287 ASP cc_start: 0.7801 (t0) cc_final: 0.7572 (t0) REVERT: C 293 LEU cc_start: 0.8451 (tp) cc_final: 0.8115 (tp) REVERT: C 300 LYS cc_start: 0.9079 (mttt) cc_final: 0.8723 (mtmm) REVERT: C 303 LEU cc_start: 0.8761 (mt) cc_final: 0.8469 (tp) REVERT: C 353 TRP cc_start: 0.5844 (p90) cc_final: 0.5533 (p90) REVERT: C 515 PHE cc_start: 0.7210 (m-10) cc_final: 0.6786 (m-80) REVERT: C 528 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.6205 (mmtm) REVERT: C 537 LYS cc_start: 0.8522 (tptt) cc_final: 0.8144 (tptp) REVERT: C 721 SER cc_start: 0.8065 (t) cc_final: 0.7747 (p) REVERT: C 752 LEU cc_start: 0.9209 (mt) cc_final: 0.8960 (tt) REVERT: C 755 GLN cc_start: 0.7462 (mt0) cc_final: 0.6868 (mp10) REVERT: C 795 LYS cc_start: 0.7440 (mttt) cc_final: 0.7235 (mttt) REVERT: C 884 SER cc_start: 0.8285 (m) cc_final: 0.8066 (t) REVERT: C 898 PHE cc_start: 0.6427 (t80) cc_final: 0.6180 (t80) REVERT: C 935 GLN cc_start: 0.8421 (tt0) cc_final: 0.7998 (tt0) REVERT: C 969 LYS cc_start: 0.8574 (mttt) cc_final: 0.8200 (mtmm) REVERT: C 1055 SER cc_start: 0.6945 (m) cc_final: 0.6456 (t) REVERT: C 1111 GLU cc_start: 0.7591 (tt0) cc_final: 0.7290 (tt0) REVERT: C 1116 THR cc_start: 0.7960 (p) cc_final: 0.7148 (p) REVERT: C 1145 LEU cc_start: 0.7569 (mt) cc_final: 0.7255 (mt) REVERT: c 34 MET cc_start: 0.5311 (mmm) cc_final: 0.4470 (mmm) REVERT: B 33 THR cc_start: 0.7988 (p) cc_final: 0.7715 (t) REVERT: B 84 LEU cc_start: 0.7912 (mt) cc_final: 0.7464 (mp) REVERT: B 133 PHE cc_start: 0.5580 (m-10) cc_final: 0.5178 (m-10) REVERT: B 200 TYR cc_start: 0.5798 (m-80) cc_final: 0.5290 (m-80) REVERT: B 237 ARG cc_start: 0.5586 (mtt-85) cc_final: 0.5386 (mtt-85) REVERT: B 340 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7650 (mp0) REVERT: B 353 TRP cc_start: 0.6165 (p90) cc_final: 0.5811 (p90) REVERT: B 384 PRO cc_start: 0.8013 (Cg_endo) cc_final: 0.7629 (Cg_exo) REVERT: B 535 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7049 (tmtt) REVERT: B 537 LYS cc_start: 0.8066 (tptt) cc_final: 0.7703 (tptp) REVERT: B 581 THR cc_start: 0.6717 (p) cc_final: 0.5215 (m) REVERT: B 583 GLU cc_start: 0.5418 (mt-10) cc_final: 0.5060 (mt-10) REVERT: B 654 GLU cc_start: 0.7698 (tt0) cc_final: 0.7418 (tt0) REVERT: B 726 ILE cc_start: 0.8793 (mp) cc_final: 0.8521 (mt) REVERT: B 730 SER cc_start: 0.8893 (p) cc_final: 0.8672 (t) REVERT: B 814 LYS cc_start: 0.8723 (mttt) cc_final: 0.8446 (mmmt) REVERT: B 884 SER cc_start: 0.7823 (m) cc_final: 0.7512 (t) REVERT: B 969 LYS cc_start: 0.8824 (mttt) cc_final: 0.8370 (mmtm) REVERT: B 979 ASP cc_start: 0.8572 (m-30) cc_final: 0.7927 (t0) REVERT: B 1000 ARG cc_start: 0.7737 (mtt180) cc_final: 0.7462 (mmt90) REVERT: a 31 ARG cc_start: 0.6126 (mmt180) cc_final: 0.5787 (mmm160) REVERT: a 38 LYS cc_start: 0.7912 (tttt) cc_final: 0.7490 (tttt) REVERT: a 64 PHE cc_start: 0.8560 (m-10) cc_final: 0.8270 (m-10) REVERT: a 69 THR cc_start: 0.6317 (m) cc_final: 0.5627 (p) REVERT: a 73 ASP cc_start: 0.7739 (t0) cc_final: 0.7532 (t0) REVERT: a 76 SER cc_start: 0.8782 (m) cc_final: 0.8570 (p) REVERT: a 78 THR cc_start: 0.8530 (m) cc_final: 0.8094 (m) REVERT: a 153 PHE cc_start: 0.8320 (t80) cc_final: 0.7716 (t80) REVERT: b 46 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7747 (mm-40) REVERT: b 145 PRO cc_start: 0.5588 (Cg_endo) cc_final: 0.5133 (Cg_exo) outliers start: 12 outliers final: 6 residues processed: 940 average time/residue: 0.4316 time to fit residues: 623.0102 Evaluate side-chains 686 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 679 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain c residue 101 TYR Chi-restraints excluded: chain d residue 53 TYR Chi-restraints excluded: chain a residue 184 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 0.0040 chunk 286 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 296 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 180 optimal weight: 0.0980 chunk 220 optimal weight: 20.0000 chunk 343 optimal weight: 0.6980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 414 GLN A 755 GLN A 895 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 207 HIS C 239 GLN C 360 ASN C 409 GLN C 519 HIS C 717 ASN C 762 GLN C 895 GLN C 901 GLN C1101 HIS c 52 HIS ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 519 HIS B 544 ASN B 717 ASN B 955 ASN B1054 GLN B1083 HIS B1106 GLN B1113 GLN b 42 GLN b 93 HIS b 194 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30457 Z= 0.182 Angle : 0.595 8.411 41433 Z= 0.313 Chirality : 0.045 0.194 4671 Planarity : 0.004 0.054 5342 Dihedral : 4.987 52.472 4101 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.87 % Favored : 98.11 % Rotamer: Outliers : 2.56 % Allowed : 9.13 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -1.61 (0.11), residues: 3749 helix: -2.64 (0.15), residues: 584 sheet: 0.33 (0.15), residues: 856 loop : -1.21 (0.11), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 104 HIS 0.006 0.001 HIS C 207 PHE 0.024 0.002 PHE C 927 TYR 0.014 0.001 TYR b 36 ARG 0.007 0.001 ARG a 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 699 time to evaluate : 3.276 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: A 206 LYS cc_start: 0.8194 (tmtt) cc_final: 0.7854 (tptt) REVERT: A 298 GLU cc_start: 0.8190 (tp30) cc_final: 0.7959 (tp30) REVERT: A 619 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7925 (mt-10) REVERT: A 654 GLU cc_start: 0.7212 (tt0) cc_final: 0.6987 (tt0) REVERT: A 655 TYR cc_start: 0.8639 (t80) cc_final: 0.8380 (t80) REVERT: A 752 LEU cc_start: 0.8981 (mt) cc_final: 0.8608 (mt) REVERT: A 882 ILE cc_start: 0.8052 (mt) cc_final: 0.7740 (mm) REVERT: A 969 LYS cc_start: 0.8613 (mttt) cc_final: 0.7945 (mmmt) REVERT: A 979 ASP cc_start: 0.7463 (m-30) cc_final: 0.6937 (t0) REVERT: A 984 LEU cc_start: 0.7955 (mt) cc_final: 0.7551 (tp) REVERT: A 985 ASP cc_start: 0.8143 (m-30) cc_final: 0.7414 (m-30) REVERT: A 1084 ASP cc_start: 0.7839 (p0) cc_final: 0.7001 (p0) REVERT: C 33 THR cc_start: 0.8057 (p) cc_final: 0.7808 (p) REVERT: C 81 ASN cc_start: 0.8335 (t0) cc_final: 0.7950 (m-40) REVERT: C 106 PHE cc_start: 0.6469 (m-10) cc_final: 0.6243 (m-10) REVERT: C 173 GLN cc_start: 0.6745 (pp30) cc_final: 0.6046 (pp30) REVERT: C 201 PHE cc_start: 0.8168 (t80) cc_final: 0.7955 (t80) REVERT: C 206 LYS cc_start: 0.8509 (tptt) cc_final: 0.8234 (tptt) REVERT: C 276 LEU cc_start: 0.8304 (tp) cc_final: 0.8082 (tt) REVERT: C 287 ASP cc_start: 0.7854 (t0) cc_final: 0.7557 (t0) REVERT: C 289 VAL cc_start: 0.8961 (t) cc_final: 0.8750 (m) REVERT: C 293 LEU cc_start: 0.8327 (tp) cc_final: 0.8066 (tp) REVERT: C 353 TRP cc_start: 0.5919 (p90) cc_final: 0.5563 (p90) REVERT: C 389 ASP cc_start: 0.8499 (m-30) cc_final: 0.8124 (p0) REVERT: C 508 TYR cc_start: 0.7002 (m-10) cc_final: 0.6769 (m-10) REVERT: C 513 LEU cc_start: 0.7959 (pp) cc_final: 0.7482 (pp) REVERT: C 528 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6525 (mmtm) REVERT: C 533 LEU cc_start: 0.8513 (tp) cc_final: 0.8306 (mt) REVERT: C 537 LYS cc_start: 0.8669 (tptt) cc_final: 0.8034 (tptp) REVERT: C 581 THR cc_start: 0.6600 (p) cc_final: 0.5753 (m) REVERT: C 656 VAL cc_start: 0.8565 (m) cc_final: 0.8268 (p) REVERT: C 737 ASP cc_start: 0.7522 (t0) cc_final: 0.6102 (t0) REVERT: C 739 THR cc_start: 0.7389 (m) cc_final: 0.7085 (m) REVERT: C 755 GLN cc_start: 0.7442 (mt0) cc_final: 0.6903 (mp10) REVERT: C 765 ARG cc_start: 0.7754 (ttp80) cc_final: 0.7473 (ttp80) REVERT: C 776 LYS cc_start: 0.8378 (ttpp) cc_final: 0.7906 (ttpp) REVERT: C 884 SER cc_start: 0.8556 (m) cc_final: 0.8257 (t) REVERT: C 898 PHE cc_start: 0.6750 (t80) cc_final: 0.6498 (t80) REVERT: C 955 ASN cc_start: 0.8254 (m-40) cc_final: 0.7854 (t0) REVERT: C 969 LYS cc_start: 0.8719 (mttt) cc_final: 0.8370 (mtmm) REVERT: C 981 PHE cc_start: 0.7017 (t80) cc_final: 0.6446 (t80) REVERT: C 1002 GLN cc_start: 0.8391 (tp40) cc_final: 0.8181 (tp40) REVERT: C 1111 GLU cc_start: 0.7871 (tt0) cc_final: 0.7512 (tt0) REVERT: C 1116 THR cc_start: 0.7441 (p) cc_final: 0.7210 (p) REVERT: C 1145 LEU cc_start: 0.7746 (mt) cc_final: 0.7446 (mt) REVERT: c 34 MET cc_start: 0.4972 (mmm) cc_final: 0.4086 (mmm) REVERT: B 66 HIS cc_start: 0.6915 (OUTLIER) cc_final: 0.6671 (t70) REVERT: B 129 LYS cc_start: 0.8035 (tptm) cc_final: 0.7807 (tptt) REVERT: B 195 LYS cc_start: 0.4943 (tptt) cc_final: 0.4310 (tptp) REVERT: B 200 TYR cc_start: 0.6032 (m-10) cc_final: 0.5447 (m-80) REVERT: B 353 TRP cc_start: 0.6372 (p90) cc_final: 0.5711 (p90) REVERT: B 384 PRO cc_start: 0.8029 (Cg_endo) cc_final: 0.7700 (Cg_exo) REVERT: B 515 PHE cc_start: 0.6771 (m-80) cc_final: 0.6451 (m-80) REVERT: B 581 THR cc_start: 0.7430 (p) cc_final: 0.6275 (m) REVERT: B 595 VAL cc_start: 0.7836 (t) cc_final: 0.7620 (p) REVERT: B 675 GLN cc_start: 0.6687 (mm-40) cc_final: 0.6240 (mm-40) REVERT: B 730 SER cc_start: 0.8999 (p) cc_final: 0.8769 (t) REVERT: B 752 LEU cc_start: 0.8634 (mt) cc_final: 0.8371 (mt) REVERT: B 775 ASP cc_start: 0.8360 (m-30) cc_final: 0.8002 (t0) REVERT: B 776 LYS cc_start: 0.8570 (mtpp) cc_final: 0.8241 (ttpp) REVERT: B 884 SER cc_start: 0.8351 (m) cc_final: 0.7941 (t) REVERT: B 900 MET cc_start: 0.8548 (mtp) cc_final: 0.8202 (mtp) REVERT: B 936 ASP cc_start: 0.7837 (m-30) cc_final: 0.7610 (t0) REVERT: B 969 LYS cc_start: 0.8949 (mttt) cc_final: 0.8478 (mmtm) REVERT: B 988 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8092 (tp30) REVERT: B 1010 GLN cc_start: 0.8213 (tp40) cc_final: 0.8011 (tp-100) REVERT: B 1110 TYR cc_start: 0.7741 (t80) cc_final: 0.7010 (t80) REVERT: B 1119 ASN cc_start: 0.7325 (m-40) cc_final: 0.7093 (m-40) REVERT: B 1146 ASP cc_start: 0.7236 (m-30) cc_final: 0.6936 (p0) REVERT: a 23 LYS cc_start: 0.7767 (tptm) cc_final: 0.7476 (tptt) REVERT: a 31 ARG cc_start: 0.6420 (mmt180) cc_final: 0.6023 (mmm160) REVERT: a 34 MET cc_start: 0.8353 (tpp) cc_final: 0.7768 (mmm) REVERT: a 61 ASN cc_start: 0.7508 (t0) cc_final: 0.7178 (t0) REVERT: a 64 PHE cc_start: 0.8683 (m-10) cc_final: 0.8482 (m-10) REVERT: a 69 THR cc_start: 0.6863 (m) cc_final: 0.6203 (p) REVERT: a 73 ASP cc_start: 0.7962 (t0) cc_final: 0.7745 (t0) REVERT: a 76 SER cc_start: 0.8991 (m) cc_final: 0.8639 (p) REVERT: a 81 MET cc_start: 0.4538 (tmm) cc_final: 0.4051 (tmm) REVERT: a 142 MET cc_start: 0.4748 (OUTLIER) cc_final: 0.4250 (mmm) REVERT: a 153 PHE cc_start: 0.8451 (t80) cc_final: 0.7584 (t80) REVERT: b 59 GLU cc_start: 0.7972 (tp30) cc_final: 0.7691 (mt-10) outliers start: 85 outliers final: 41 residues processed: 751 average time/residue: 0.4170 time to fit residues: 488.9205 Evaluate side-chains 678 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 634 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain c residue 101 TYR Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain d residue 53 TYR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 142 MET Chi-restraints excluded: chain a residue 184 LEU Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 50 LEU Chi-restraints excluded: chain b residue 152 TRP Chi-restraints excluded: chain b residue 182 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 285 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 343 optimal weight: 7.9990 chunk 371 optimal weight: 8.9990 chunk 306 optimal weight: 2.9990 chunk 341 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 275 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 207 HIS A 394 ASN A 414 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 360 ASN B 613 GLN B 895 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 30457 Z= 0.377 Angle : 0.712 9.511 41433 Z= 0.378 Chirality : 0.048 0.280 4671 Planarity : 0.005 0.061 5342 Dihedral : 5.219 50.836 4099 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.28 % Rotamer: Outliers : 4.04 % Allowed : 10.27 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -1.02 (0.12), residues: 3749 helix: -0.91 (0.19), residues: 610 sheet: 0.42 (0.16), residues: 864 loop : -1.06 (0.12), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 64 HIS 0.036 0.003 HIS B 66 PHE 0.033 0.003 PHE C 543 TYR 0.032 0.002 TYR C 380 ARG 0.015 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 706 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.7471 (m) cc_final: 0.7146 (m) REVERT: A 160 TYR cc_start: 0.7277 (p90) cc_final: 0.6755 (p90) REVERT: A 169 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8126 (mp0) REVERT: A 206 LYS cc_start: 0.8708 (tmtt) cc_final: 0.8116 (tptp) REVERT: A 298 GLU cc_start: 0.8531 (tp30) cc_final: 0.8199 (tp30) REVERT: A 592 PHE cc_start: 0.7834 (p90) cc_final: 0.7450 (p90) REVERT: A 615 VAL cc_start: 0.8695 (t) cc_final: 0.8436 (m) REVERT: A 616 ASN cc_start: 0.6632 (m-40) cc_final: 0.6423 (m-40) REVERT: A 654 GLU cc_start: 0.7329 (tt0) cc_final: 0.7030 (tt0) REVERT: A 655 TYR cc_start: 0.8774 (t80) cc_final: 0.8359 (t80) REVERT: A 663 ASP cc_start: 0.7168 (m-30) cc_final: 0.6960 (m-30) REVERT: A 752 LEU cc_start: 0.9015 (mt) cc_final: 0.8674 (mt) REVERT: A 859 THR cc_start: 0.8103 (t) cc_final: 0.7717 (p) REVERT: A 872 GLN cc_start: 0.7878 (tt0) cc_final: 0.7676 (tt0) REVERT: A 914 ASN cc_start: 0.8508 (m-40) cc_final: 0.7690 (m-40) REVERT: A 935 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8403 (tm-30) REVERT: A 950 ASP cc_start: 0.7158 (t0) cc_final: 0.6882 (t0) REVERT: A 964 LYS cc_start: 0.8671 (mmmm) cc_final: 0.8426 (mmmt) REVERT: A 969 LYS cc_start: 0.9009 (mttt) cc_final: 0.8393 (mmtt) REVERT: A 979 ASP cc_start: 0.8001 (m-30) cc_final: 0.7426 (t0) REVERT: A 984 LEU cc_start: 0.8000 (mt) cc_final: 0.7666 (tp) REVERT: A 985 ASP cc_start: 0.8299 (m-30) cc_final: 0.7691 (m-30) REVERT: A 990 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7909 (pp20) REVERT: A 1041 ASP cc_start: 0.8186 (m-30) cc_final: 0.7889 (m-30) REVERT: A 1084 ASP cc_start: 0.8106 (p0) cc_final: 0.7863 (p0) REVERT: C 33 THR cc_start: 0.8188 (p) cc_final: 0.7953 (p) REVERT: C 81 ASN cc_start: 0.8489 (t0) cc_final: 0.8238 (m-40) REVERT: C 106 PHE cc_start: 0.7263 (m-80) cc_final: 0.6794 (m-10) REVERT: C 128 ILE cc_start: 0.8315 (mm) cc_final: 0.7752 (mp) REVERT: C 173 GLN cc_start: 0.7068 (pp30) cc_final: 0.6521 (pp30) REVERT: C 206 LYS cc_start: 0.8337 (tptt) cc_final: 0.7447 (tppt) REVERT: C 238 PHE cc_start: 0.7979 (p90) cc_final: 0.7665 (p90) REVERT: C 275 PHE cc_start: 0.8149 (m-80) cc_final: 0.7765 (m-80) REVERT: C 277 LEU cc_start: 0.8399 (mt) cc_final: 0.7976 (mm) REVERT: C 289 VAL cc_start: 0.8941 (t) cc_final: 0.8657 (p) REVERT: C 303 LEU cc_start: 0.8998 (mt) cc_final: 0.8690 (tt) REVERT: C 324 GLU cc_start: 0.4181 (mm-30) cc_final: 0.3945 (mm-30) REVERT: C 389 ASP cc_start: 0.8629 (m-30) cc_final: 0.8148 (p0) REVERT: C 528 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6492 (mmtm) REVERT: C 537 LYS cc_start: 0.8733 (tptt) cc_final: 0.7968 (tptm) REVERT: C 547 LYS cc_start: 0.7877 (mttt) cc_final: 0.7419 (mmtp) REVERT: C 595 VAL cc_start: 0.8075 (t) cc_final: 0.7688 (p) REVERT: C 651 ILE cc_start: 0.8831 (mp) cc_final: 0.8596 (mp) REVERT: C 656 VAL cc_start: 0.8829 (m) cc_final: 0.8542 (p) REVERT: C 740 MET cc_start: 0.7188 (mpp) cc_final: 0.6941 (mmp) REVERT: C 765 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7658 (ttp80) REVERT: C 776 LYS cc_start: 0.8392 (ttpp) cc_final: 0.7970 (ttpp) REVERT: C 800 PHE cc_start: 0.7487 (m-10) cc_final: 0.7236 (m-10) REVERT: C 817 PHE cc_start: 0.8046 (t80) cc_final: 0.7751 (t80) REVERT: C 950 ASP cc_start: 0.7831 (t0) cc_final: 0.7361 (t0) REVERT: C 969 LYS cc_start: 0.8990 (mttt) cc_final: 0.8670 (mtmm) REVERT: C 979 ASP cc_start: 0.8111 (m-30) cc_final: 0.7638 (m-30) REVERT: C 1002 GLN cc_start: 0.8523 (tp40) cc_final: 0.8093 (tp40) REVERT: C 1111 GLU cc_start: 0.8366 (tt0) cc_final: 0.8083 (tt0) REVERT: C 1139 ASP cc_start: 0.8286 (t0) cc_final: 0.7973 (t0) REVERT: c 34 MET cc_start: 0.4942 (mmm) cc_final: 0.3985 (mmm) REVERT: B 80 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6964 (p0) REVERT: B 141 LEU cc_start: 0.5141 (mt) cc_final: 0.4560 (mp) REVERT: B 192 PHE cc_start: 0.7470 (m-10) cc_final: 0.7055 (m-10) REVERT: B 195 LYS cc_start: 0.6527 (tptt) cc_final: 0.5576 (tppt) REVERT: B 206 LYS cc_start: 0.7782 (tppt) cc_final: 0.7365 (tptp) REVERT: B 271 GLN cc_start: 0.8074 (mm110) cc_final: 0.7865 (mm-40) REVERT: B 353 TRP cc_start: 0.6985 (p90) cc_final: 0.6395 (p90) REVERT: B 355 ARG cc_start: 0.8038 (ttt180) cc_final: 0.7352 (tpp80) REVERT: B 384 PRO cc_start: 0.8372 (Cg_endo) cc_final: 0.8135 (Cg_exo) REVERT: B 515 PHE cc_start: 0.7483 (m-80) cc_final: 0.7155 (m-80) REVERT: B 557 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7912 (mttt) REVERT: B 580 GLN cc_start: 0.8628 (tt0) cc_final: 0.8274 (tp40) REVERT: B 675 GLN cc_start: 0.6755 (mm-40) cc_final: 0.6265 (mm-40) REVERT: B 737 ASP cc_start: 0.7950 (t0) cc_final: 0.7666 (t0) REVERT: B 739 THR cc_start: 0.7579 (m) cc_final: 0.7209 (p) REVERT: B 814 LYS cc_start: 0.8584 (mmmt) cc_final: 0.8187 (mmmt) REVERT: B 868 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7704 (tm-30) REVERT: B 884 SER cc_start: 0.8861 (m) cc_final: 0.8216 (t) REVERT: B 918 GLU cc_start: 0.8282 (mp0) cc_final: 0.7804 (mp0) REVERT: B 936 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7535 (t0) REVERT: B 969 LYS cc_start: 0.9072 (mttt) cc_final: 0.8498 (mttm) REVERT: B 995 ARG cc_start: 0.7891 (tpp80) cc_final: 0.7548 (ttp80) REVERT: B 1050 MET cc_start: 0.8741 (ptp) cc_final: 0.8346 (ptp) REVERT: B 1119 ASN cc_start: 0.7506 (m-40) cc_final: 0.7066 (m-40) REVERT: B 1125 ASN cc_start: 0.8241 (p0) cc_final: 0.7829 (p0) REVERT: B 1127 ASP cc_start: 0.7932 (p0) cc_final: 0.7524 (p0) REVERT: a 34 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7716 (mpp) REVERT: a 36 TRP cc_start: 0.7650 (m100) cc_final: 0.7086 (m100) REVERT: a 61 ASN cc_start: 0.7736 (t0) cc_final: 0.7386 (t0) REVERT: a 71 THR cc_start: 0.7847 (m) cc_final: 0.7205 (p) REVERT: a 76 SER cc_start: 0.9114 (m) cc_final: 0.8803 (p) REVERT: a 153 PHE cc_start: 0.8539 (t80) cc_final: 0.8042 (t80) REVERT: b 44 PRO cc_start: 0.8554 (Cg_endo) cc_final: 0.8114 (Cg_exo) REVERT: b 91 TYR cc_start: 0.7508 (m-80) cc_final: 0.7223 (m-80) REVERT: b 167 TRP cc_start: 0.7924 (p90) cc_final: 0.7639 (p90) outliers start: 134 outliers final: 83 residues processed: 770 average time/residue: 0.4346 time to fit residues: 522.2559 Evaluate side-chains 720 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 632 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain c residue 101 TYR Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain d residue 53 TYR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain a residue 34 MET Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 184 LEU Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 50 LEU Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 152 TRP Chi-restraints excluded: chain b residue 182 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 4.9990 chunk 258 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 164 optimal weight: 0.0170 chunk 230 optimal weight: 6.9990 chunk 345 optimal weight: 8.9990 chunk 365 optimal weight: 8.9990 chunk 180 optimal weight: 0.9990 chunk 327 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C 949 GLN C 957 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 30457 Z= 0.261 Angle : 0.597 12.126 41433 Z= 0.308 Chirality : 0.045 0.217 4671 Planarity : 0.004 0.065 5342 Dihedral : 4.917 50.987 4099 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 3.40 % Allowed : 13.86 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 3749 helix: 0.06 (0.21), residues: 618 sheet: 0.49 (0.16), residues: 875 loop : -1.02 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 104 HIS 0.018 0.002 HIS A 207 PHE 0.048 0.002 PHE C 342 TYR 0.025 0.001 TYR C 380 ARG 0.006 0.001 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 658 time to evaluate : 3.516 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: A 160 TYR cc_start: 0.7346 (p90) cc_final: 0.6757 (p90) REVERT: A 206 LYS cc_start: 0.8790 (tmtt) cc_final: 0.8168 (tptp) REVERT: A 270 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.7736 (mm) REVERT: A 271 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8119 (mm-40) REVERT: A 298 GLU cc_start: 0.8499 (tp30) cc_final: 0.7884 (tp30) REVERT: A 574 ASP cc_start: 0.5982 (p0) cc_final: 0.5765 (t0) REVERT: A 606 ASN cc_start: 0.9237 (OUTLIER) cc_final: 0.9032 (t0) REVERT: A 615 VAL cc_start: 0.8952 (t) cc_final: 0.8588 (p) REVERT: A 654 GLU cc_start: 0.7279 (tt0) cc_final: 0.6954 (tt0) REVERT: A 655 TYR cc_start: 0.8750 (t80) cc_final: 0.8444 (t80) REVERT: A 663 ASP cc_start: 0.7012 (m-30) cc_final: 0.6792 (m-30) REVERT: A 740 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7819 (tpp) REVERT: A 752 LEU cc_start: 0.9000 (mt) cc_final: 0.8672 (mt) REVERT: A 776 LYS cc_start: 0.8399 (ttmm) cc_final: 0.7884 (ttmm) REVERT: A 823 PHE cc_start: 0.8548 (t80) cc_final: 0.8242 (t80) REVERT: A 872 GLN cc_start: 0.7806 (tt0) cc_final: 0.7595 (tt0) REVERT: A 914 ASN cc_start: 0.8332 (m-40) cc_final: 0.7880 (m-40) REVERT: A 935 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8438 (tm-30) REVERT: A 937 SER cc_start: 0.9049 (m) cc_final: 0.8791 (t) REVERT: A 950 ASP cc_start: 0.7140 (t0) cc_final: 0.6833 (t0) REVERT: A 955 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8297 (t0) REVERT: A 964 LYS cc_start: 0.8747 (mmmm) cc_final: 0.8335 (mmmt) REVERT: A 969 LYS cc_start: 0.8997 (mttt) cc_final: 0.8306 (mmmt) REVERT: A 979 ASP cc_start: 0.7972 (m-30) cc_final: 0.7567 (t0) REVERT: A 984 LEU cc_start: 0.8231 (mt) cc_final: 0.7693 (tp) REVERT: A 985 ASP cc_start: 0.8381 (m-30) cc_final: 0.7828 (m-30) REVERT: A 1072 GLU cc_start: 0.8379 (pm20) cc_final: 0.8140 (pm20) REVERT: A 1111 GLU cc_start: 0.8498 (tt0) cc_final: 0.8183 (mt-10) REVERT: C 33 THR cc_start: 0.8150 (p) cc_final: 0.7930 (p) REVERT: C 64 TRP cc_start: 0.8206 (t60) cc_final: 0.8000 (t60) REVERT: C 128 ILE cc_start: 0.8430 (mm) cc_final: 0.7961 (mp) REVERT: C 173 GLN cc_start: 0.7057 (pp30) cc_final: 0.6565 (pp30) REVERT: C 226 LEU cc_start: 0.8042 (pp) cc_final: 0.7723 (pt) REVERT: C 275 PHE cc_start: 0.8349 (m-80) cc_final: 0.8047 (m-80) REVERT: C 289 VAL cc_start: 0.8954 (t) cc_final: 0.8664 (p) REVERT: C 389 ASP cc_start: 0.8684 (m-30) cc_final: 0.8225 (p0) REVERT: C 515 PHE cc_start: 0.7552 (m-80) cc_final: 0.7351 (m-80) REVERT: C 528 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7121 (mmtm) REVERT: C 537 LYS cc_start: 0.8665 (tptt) cc_final: 0.8160 (tptm) REVERT: C 656 VAL cc_start: 0.8736 (m) cc_final: 0.8414 (p) REVERT: C 739 THR cc_start: 0.7513 (OUTLIER) cc_final: 0.7145 (t) REVERT: C 776 LYS cc_start: 0.8351 (ttpp) cc_final: 0.7957 (ttpp) REVERT: C 815 ARG cc_start: 0.8461 (mtt90) cc_final: 0.8027 (mtt180) REVERT: C 884 SER cc_start: 0.8787 (m) cc_final: 0.8368 (t) REVERT: C 957 GLN cc_start: 0.8267 (tt0) cc_final: 0.7579 (tm-30) REVERT: C 969 LYS cc_start: 0.8991 (mttt) cc_final: 0.8675 (mtmm) REVERT: C 1031 GLU cc_start: 0.7668 (mp0) cc_final: 0.7423 (mp0) REVERT: C 1111 GLU cc_start: 0.8425 (tt0) cc_final: 0.8161 (tt0) REVERT: C 1125 ASN cc_start: 0.8333 (p0) cc_final: 0.8067 (p0) REVERT: C 1139 ASP cc_start: 0.8294 (t0) cc_final: 0.7990 (t0) REVERT: c 34 MET cc_start: 0.4967 (mmm) cc_final: 0.4028 (mmm) REVERT: B 97 LYS cc_start: 0.6102 (OUTLIER) cc_final: 0.5488 (mmpt) REVERT: B 206 LYS cc_start: 0.7869 (tppt) cc_final: 0.7582 (tptp) REVERT: B 224 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6225 (mm-30) REVERT: B 271 GLN cc_start: 0.8215 (mm110) cc_final: 0.7903 (mm-40) REVERT: B 304 LYS cc_start: 0.8712 (mttt) cc_final: 0.8472 (mmtt) REVERT: B 353 TRP cc_start: 0.6953 (p90) cc_final: 0.6741 (p90) REVERT: B 357 ARG cc_start: 0.7941 (ttp-170) cc_final: 0.7126 (ttp-170) REVERT: B 384 PRO cc_start: 0.8354 (Cg_endo) cc_final: 0.8133 (Cg_exo) REVERT: B 580 GLN cc_start: 0.8648 (tt0) cc_final: 0.8409 (tp40) REVERT: B 675 GLN cc_start: 0.6911 (mm-40) cc_final: 0.6500 (mm-40) REVERT: B 737 ASP cc_start: 0.7994 (t0) cc_final: 0.7770 (t0) REVERT: B 739 THR cc_start: 0.7688 (m) cc_final: 0.7359 (p) REVERT: B 868 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7539 (tm-30) REVERT: B 884 SER cc_start: 0.8793 (m) cc_final: 0.8185 (t) REVERT: B 918 GLU cc_start: 0.8379 (mp0) cc_final: 0.7718 (mp0) REVERT: B 969 LYS cc_start: 0.9060 (mttt) cc_final: 0.8480 (mtpp) REVERT: B 988 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8134 (tp30) REVERT: B 995 ARG cc_start: 0.7790 (tpp80) cc_final: 0.7486 (ttp80) REVERT: B 1041 ASP cc_start: 0.7753 (m-30) cc_final: 0.7159 (m-30) REVERT: B 1045 LYS cc_start: 0.8366 (mmmm) cc_final: 0.7733 (mmmm) REVERT: B 1050 MET cc_start: 0.8725 (ptp) cc_final: 0.8320 (ptp) REVERT: B 1119 ASN cc_start: 0.7372 (m-40) cc_final: 0.6921 (m-40) REVERT: a 36 TRP cc_start: 0.7632 (m100) cc_final: 0.6884 (m100) REVERT: a 71 THR cc_start: 0.8003 (m) cc_final: 0.7739 (t) REVERT: a 76 SER cc_start: 0.9071 (m) cc_final: 0.8849 (p) REVERT: a 85 SER cc_start: 0.8001 (t) cc_final: 0.7552 (p) REVERT: a 153 PHE cc_start: 0.8348 (t80) cc_final: 0.7746 (t80) REVERT: a 154 PRO cc_start: 0.8688 (Cg_endo) cc_final: 0.8389 (Cg_exo) REVERT: b 62 VAL cc_start: 0.9073 (t) cc_final: 0.8539 (p) REVERT: b 91 TYR cc_start: 0.7586 (m-80) cc_final: 0.7260 (m-80) REVERT: b 107 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.5634 (mmmt) REVERT: b 167 TRP cc_start: 0.7841 (p90) cc_final: 0.7616 (p90) outliers start: 113 outliers final: 73 residues processed: 713 average time/residue: 0.4376 time to fit residues: 488.6924 Evaluate side-chains 705 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 623 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain c residue 101 TYR Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain d residue 53 TYR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 123 THR Chi-restraints excluded: chain a residue 184 LEU Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 50 LEU Chi-restraints excluded: chain b residue 107 LYS Chi-restraints excluded: chain b residue 152 TRP Chi-restraints excluded: chain b residue 182 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 0.0070 chunk 207 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 311 optimal weight: 0.6980 chunk 252 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 327 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 779 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30457 Z= 0.256 Angle : 0.589 9.465 41433 Z= 0.304 Chirality : 0.045 0.212 4671 Planarity : 0.004 0.050 5342 Dihedral : 4.816 53.700 4099 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.04 % Rotamer: Outliers : 3.50 % Allowed : 15.25 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.13), residues: 3749 helix: 0.56 (0.22), residues: 618 sheet: 0.45 (0.16), residues: 887 loop : -0.97 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP a 161 HIS 0.009 0.001 HIS C 207 PHE 0.037 0.002 PHE C 338 TYR 0.014 0.001 TYR A1138 ARG 0.009 0.001 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 642 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.7381 (p90) cc_final: 0.6808 (p90) REVERT: A 169 GLU cc_start: 0.7859 (mp0) cc_final: 0.7607 (mm-30) REVERT: A 206 LYS cc_start: 0.8777 (tmtt) cc_final: 0.8185 (tptp) REVERT: A 270 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7808 (mm) REVERT: A 271 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8174 (mm-40) REVERT: A 567 ARG cc_start: 0.6813 (mtm180) cc_final: 0.6530 (mtm180) REVERT: A 606 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8624 (t0) REVERT: A 655 TYR cc_start: 0.8711 (t80) cc_final: 0.8451 (t80) REVERT: A 740 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7941 (tpp) REVERT: A 752 LEU cc_start: 0.8985 (mt) cc_final: 0.8522 (mt) REVERT: A 779 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8196 (tp40) REVERT: A 823 PHE cc_start: 0.8516 (t80) cc_final: 0.8310 (t80) REVERT: A 868 GLU cc_start: 0.7903 (tt0) cc_final: 0.7697 (tm-30) REVERT: A 872 GLN cc_start: 0.7830 (tt0) cc_final: 0.7504 (tt0) REVERT: A 900 MET cc_start: 0.8371 (ptp) cc_final: 0.8160 (ptp) REVERT: A 914 ASN cc_start: 0.8373 (m-40) cc_final: 0.7988 (m-40) REVERT: A 935 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8539 (tm-30) REVERT: A 937 SER cc_start: 0.9047 (m) cc_final: 0.8780 (t) REVERT: A 950 ASP cc_start: 0.7176 (t0) cc_final: 0.6728 (t0) REVERT: A 955 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8232 (t0) REVERT: A 964 LYS cc_start: 0.8756 (mmmm) cc_final: 0.8446 (mmmt) REVERT: A 969 LYS cc_start: 0.8944 (mttt) cc_final: 0.8275 (mmmt) REVERT: A 979 ASP cc_start: 0.8024 (m-30) cc_final: 0.7658 (t0) REVERT: A 984 LEU cc_start: 0.8167 (mt) cc_final: 0.7662 (tp) REVERT: A 985 ASP cc_start: 0.8437 (m-30) cc_final: 0.7769 (p0) REVERT: A 990 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7851 (tp30) REVERT: A 1107 ARG cc_start: 0.7887 (mtt90) cc_final: 0.7389 (mtt90) REVERT: A 1111 GLU cc_start: 0.8463 (tt0) cc_final: 0.8205 (mt-10) REVERT: C 52 GLN cc_start: 0.7503 (tm-30) cc_final: 0.7223 (tm-30) REVERT: C 106 PHE cc_start: 0.7439 (m-80) cc_final: 0.7056 (m-80) REVERT: C 128 ILE cc_start: 0.8456 (mm) cc_final: 0.8022 (mp) REVERT: C 173 GLN cc_start: 0.7104 (pp30) cc_final: 0.6513 (pp30) REVERT: C 206 LYS cc_start: 0.8349 (tptt) cc_final: 0.7956 (tppt) REVERT: C 224 GLU cc_start: 0.6622 (mp0) cc_final: 0.6237 (mp0) REVERT: C 237 ARG cc_start: 0.7609 (mtm180) cc_final: 0.7095 (mtm110) REVERT: C 275 PHE cc_start: 0.8260 (m-80) cc_final: 0.7895 (m-80) REVERT: C 289 VAL cc_start: 0.8906 (t) cc_final: 0.8623 (p) REVERT: C 298 GLU cc_start: 0.8378 (tp30) cc_final: 0.7985 (tp30) REVERT: C 356 LYS cc_start: 0.8719 (ttpt) cc_final: 0.8339 (ttmt) REVERT: C 389 ASP cc_start: 0.8706 (m-30) cc_final: 0.8216 (p0) REVERT: C 498 ARG cc_start: 0.7116 (tpp80) cc_final: 0.6907 (tpp80) REVERT: C 515 PHE cc_start: 0.7484 (m-80) cc_final: 0.7244 (m-80) REVERT: C 528 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7181 (mmtm) REVERT: C 537 LYS cc_start: 0.8698 (tptt) cc_final: 0.8205 (tptm) REVERT: C 577 ARG cc_start: 0.6645 (ttp80) cc_final: 0.6425 (ttp-170) REVERT: C 613 GLN cc_start: 0.7911 (pt0) cc_final: 0.7679 (pt0) REVERT: C 644 GLN cc_start: 0.6944 (tp-100) cc_final: 0.6668 (tp-100) REVERT: C 776 LYS cc_start: 0.8342 (ttpp) cc_final: 0.7951 (ttpp) REVERT: C 815 ARG cc_start: 0.8428 (mtt90) cc_final: 0.8117 (mtt180) REVERT: C 816 SER cc_start: 0.8461 (p) cc_final: 0.7799 (t) REVERT: C 884 SER cc_start: 0.8785 (m) cc_final: 0.8238 (t) REVERT: C 957 GLN cc_start: 0.8251 (tt0) cc_final: 0.7918 (tm-30) REVERT: C 969 LYS cc_start: 0.9020 (mttt) cc_final: 0.8694 (mtmm) REVERT: C 1031 GLU cc_start: 0.7597 (mp0) cc_final: 0.7032 (mp0) REVERT: C 1111 GLU cc_start: 0.8397 (tt0) cc_final: 0.8163 (tt0) REVERT: C 1139 ASP cc_start: 0.8362 (t0) cc_final: 0.8074 (t0) REVERT: c 34 MET cc_start: 0.4911 (mmm) cc_final: 0.3977 (mmm) REVERT: B 79 PHE cc_start: 0.7312 (m-80) cc_final: 0.7039 (m-80) REVERT: B 97 LYS cc_start: 0.5855 (OUTLIER) cc_final: 0.5163 (mmpt) REVERT: B 203 ILE cc_start: 0.8758 (mt) cc_final: 0.8413 (pt) REVERT: B 206 LYS cc_start: 0.7827 (tppt) cc_final: 0.7564 (tptp) REVERT: B 271 GLN cc_start: 0.8276 (mm110) cc_final: 0.7991 (mm110) REVERT: B 338 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.8220 (m-10) REVERT: B 384 PRO cc_start: 0.8367 (Cg_endo) cc_final: 0.8162 (Cg_exo) REVERT: B 508 TYR cc_start: 0.7100 (m-80) cc_final: 0.6815 (m-80) REVERT: B 675 GLN cc_start: 0.6815 (mm-40) cc_final: 0.6458 (mm-40) REVERT: B 814 LYS cc_start: 0.8392 (mmmt) cc_final: 0.8093 (mmmt) REVERT: B 819 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7517 (mt-10) REVERT: B 868 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7502 (tm-30) REVERT: B 884 SER cc_start: 0.8773 (m) cc_final: 0.8241 (t) REVERT: B 902 MET cc_start: 0.8296 (mmm) cc_final: 0.7466 (mmt) REVERT: B 918 GLU cc_start: 0.8427 (mp0) cc_final: 0.7806 (mp0) REVERT: B 936 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7572 (t0) REVERT: B 969 LYS cc_start: 0.9063 (mttt) cc_final: 0.8526 (mttm) REVERT: B 988 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8170 (tp30) REVERT: B 995 ARG cc_start: 0.7809 (tpp80) cc_final: 0.7448 (ttp80) REVERT: B 1017 GLU cc_start: 0.8239 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B 1041 ASP cc_start: 0.7821 (m-30) cc_final: 0.7112 (m-30) REVERT: B 1045 LYS cc_start: 0.8328 (mmmm) cc_final: 0.7669 (mmmm) REVERT: B 1050 MET cc_start: 0.8732 (ptp) cc_final: 0.8310 (ptp) REVERT: B 1119 ASN cc_start: 0.7411 (m-40) cc_final: 0.7028 (m-40) REVERT: a 34 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7766 (mpp) REVERT: a 36 TRP cc_start: 0.7707 (m100) cc_final: 0.7412 (m100) REVERT: a 85 SER cc_start: 0.8005 (t) cc_final: 0.7561 (p) REVERT: a 153 PHE cc_start: 0.8426 (t80) cc_final: 0.7449 (t80) REVERT: a 154 PRO cc_start: 0.8718 (Cg_endo) cc_final: 0.8485 (Cg_exo) REVERT: b 107 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.5591 (mmmt) REVERT: b 167 TRP cc_start: 0.7885 (p90) cc_final: 0.7652 (p90) outliers start: 116 outliers final: 86 residues processed: 697 average time/residue: 0.4569 time to fit residues: 491.1404 Evaluate side-chains 702 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 606 time to evaluate : 3.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 101 TYR Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain d residue 53 TYR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 34 MET Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 184 LEU Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 107 LYS Chi-restraints excluded: chain b residue 152 TRP Chi-restraints excluded: chain b residue 182 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 0.8980 chunk 329 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 214 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 365 optimal weight: 9.9990 chunk 303 optimal weight: 0.0970 chunk 169 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 192 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN B1074 ASN B1113 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.6622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30457 Z= 0.196 Angle : 0.562 10.262 41433 Z= 0.287 Chirality : 0.044 0.207 4671 Planarity : 0.004 0.056 5342 Dihedral : 4.675 56.026 4098 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 3.53 % Allowed : 15.85 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 3749 helix: 0.78 (0.22), residues: 636 sheet: 0.57 (0.17), residues: 845 loop : -0.93 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 104 HIS 0.016 0.001 HIS C 207 PHE 0.042 0.002 PHE C 338 TYR 0.034 0.001 TYR C 365 ARG 0.010 0.001 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 635 time to evaluate : 3.302 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: A 138 ASP cc_start: 0.8235 (t0) cc_final: 0.7926 (t0) REVERT: A 160 TYR cc_start: 0.7394 (p90) cc_final: 0.6826 (p90) REVERT: A 190 ARG cc_start: 0.7222 (mtt180) cc_final: 0.6726 (mtt180) REVERT: A 206 LYS cc_start: 0.8746 (tmtt) cc_final: 0.8162 (tptp) REVERT: A 221 SER cc_start: 0.8657 (t) cc_final: 0.8242 (p) REVERT: A 270 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.7790 (mm) REVERT: A 271 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8133 (mm-40) REVERT: A 574 ASP cc_start: 0.6166 (p0) cc_final: 0.5742 (t0) REVERT: A 606 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8606 (t0) REVERT: A 655 TYR cc_start: 0.8696 (t80) cc_final: 0.8367 (t80) REVERT: A 740 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7865 (tpp) REVERT: A 752 LEU cc_start: 0.8969 (mt) cc_final: 0.8552 (mt) REVERT: A 779 GLN cc_start: 0.8506 (tp-100) cc_final: 0.7787 (tm-30) REVERT: A 823 PHE cc_start: 0.8413 (t80) cc_final: 0.8067 (t80) REVERT: A 872 GLN cc_start: 0.7811 (tt0) cc_final: 0.7576 (tt0) REVERT: A 900 MET cc_start: 0.8390 (ptp) cc_final: 0.8151 (ptp) REVERT: A 914 ASN cc_start: 0.8371 (m-40) cc_final: 0.7977 (m-40) REVERT: A 935 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8606 (tm-30) REVERT: A 937 SER cc_start: 0.9038 (m) cc_final: 0.8767 (t) REVERT: A 950 ASP cc_start: 0.7180 (t0) cc_final: 0.6689 (t0) REVERT: A 955 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8231 (t0) REVERT: A 964 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8361 (mmmt) REVERT: A 969 LYS cc_start: 0.8977 (mttt) cc_final: 0.8348 (mmtt) REVERT: A 979 ASP cc_start: 0.7946 (m-30) cc_final: 0.7586 (t0) REVERT: A 984 LEU cc_start: 0.8163 (mt) cc_final: 0.7757 (tp) REVERT: A 985 ASP cc_start: 0.8448 (m-30) cc_final: 0.7925 (p0) REVERT: A 990 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7818 (tp30) REVERT: A 1002 GLN cc_start: 0.8042 (tp40) cc_final: 0.7641 (mm-40) REVERT: A 1045 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8306 (tptp) REVERT: A 1111 GLU cc_start: 0.8406 (tt0) cc_final: 0.8155 (mt-10) REVERT: C 52 GLN cc_start: 0.7600 (tm-30) cc_final: 0.7255 (tm-30) REVERT: C 92 PHE cc_start: 0.7615 (t80) cc_final: 0.7214 (t80) REVERT: C 106 PHE cc_start: 0.7414 (m-80) cc_final: 0.7035 (m-80) REVERT: C 173 GLN cc_start: 0.7082 (pp30) cc_final: 0.6504 (pp30) REVERT: C 189 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7864 (pp) REVERT: C 206 LYS cc_start: 0.8274 (tptt) cc_final: 0.7759 (tptt) REVERT: C 207 HIS cc_start: 0.7946 (t-170) cc_final: 0.7553 (t-170) REVERT: C 237 ARG cc_start: 0.7599 (mtm180) cc_final: 0.7291 (mtm180) REVERT: C 269 TYR cc_start: 0.7990 (m-80) cc_final: 0.7344 (m-80) REVERT: C 289 VAL cc_start: 0.8916 (t) cc_final: 0.8589 (p) REVERT: C 298 GLU cc_start: 0.8359 (tp30) cc_final: 0.7921 (tp30) REVERT: C 304 LYS cc_start: 0.8908 (mttt) cc_final: 0.8451 (mmmm) REVERT: C 309 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7654 (mt-10) REVERT: C 356 LYS cc_start: 0.8653 (ttpt) cc_final: 0.8245 (ttmt) REVERT: C 389 ASP cc_start: 0.8706 (m-30) cc_final: 0.8367 (p0) REVERT: C 498 ARG cc_start: 0.7022 (tpp80) cc_final: 0.6780 (tpp80) REVERT: C 515 PHE cc_start: 0.7414 (m-80) cc_final: 0.7168 (m-80) REVERT: C 537 LYS cc_start: 0.8637 (tptt) cc_final: 0.8127 (tptm) REVERT: C 613 GLN cc_start: 0.7898 (pt0) cc_final: 0.7635 (pt0) REVERT: C 644 GLN cc_start: 0.6994 (tp-100) cc_final: 0.6695 (tp-100) REVERT: C 745 ASP cc_start: 0.6853 (m-30) cc_final: 0.6510 (t70) REVERT: C 776 LYS cc_start: 0.8350 (ttpp) cc_final: 0.8033 (ttpp) REVERT: C 815 ARG cc_start: 0.8419 (mtt90) cc_final: 0.8061 (mtt180) REVERT: C 816 SER cc_start: 0.8478 (p) cc_final: 0.8001 (t) REVERT: C 884 SER cc_start: 0.8721 (m) cc_final: 0.8243 (t) REVERT: C 969 LYS cc_start: 0.9041 (mttt) cc_final: 0.8722 (mtmm) REVERT: C 979 ASP cc_start: 0.8226 (m-30) cc_final: 0.7704 (m-30) REVERT: C 1002 GLN cc_start: 0.8154 (tp40) cc_final: 0.7617 (tm-30) REVERT: C 1111 GLU cc_start: 0.8310 (tt0) cc_final: 0.8094 (tt0) REVERT: C 1139 ASP cc_start: 0.8338 (t0) cc_final: 0.8024 (t0) REVERT: c 34 MET cc_start: 0.4893 (mmm) cc_final: 0.3963 (mmm) REVERT: B 64 TRP cc_start: 0.6917 (t60) cc_final: 0.6652 (t60) REVERT: B 97 LYS cc_start: 0.5769 (OUTLIER) cc_final: 0.4974 (mmpt) REVERT: B 190 ARG cc_start: 0.4501 (ttt180) cc_final: 0.3484 (ttm170) REVERT: B 195 LYS cc_start: 0.6713 (tptt) cc_final: 0.6328 (tptt) REVERT: B 203 ILE cc_start: 0.8723 (mt) cc_final: 0.8373 (pt) REVERT: B 206 LYS cc_start: 0.7805 (tppt) cc_final: 0.7579 (tptp) REVERT: B 271 GLN cc_start: 0.8315 (mm110) cc_final: 0.8009 (mm-40) REVERT: B 329 PHE cc_start: 0.6405 (m-80) cc_final: 0.6194 (m-80) REVERT: B 353 TRP cc_start: 0.5211 (p90) cc_final: 0.4834 (p90) REVERT: B 508 TYR cc_start: 0.7189 (m-80) cc_final: 0.6877 (m-80) REVERT: B 580 GLN cc_start: 0.7852 (tp40) cc_final: 0.7560 (tp40) REVERT: B 675 GLN cc_start: 0.6819 (mm-40) cc_final: 0.6466 (mm-40) REVERT: B 787 GLN cc_start: 0.8203 (mp10) cc_final: 0.7952 (mp10) REVERT: B 814 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8118 (mmmt) REVERT: B 819 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7500 (mt-10) REVERT: B 868 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7409 (tm-30) REVERT: B 884 SER cc_start: 0.8767 (m) cc_final: 0.8248 (t) REVERT: B 902 MET cc_start: 0.8273 (mmm) cc_final: 0.7796 (mmm) REVERT: B 918 GLU cc_start: 0.8444 (mp0) cc_final: 0.7812 (mp0) REVERT: B 936 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7557 (t0) REVERT: B 969 LYS cc_start: 0.9071 (mttt) cc_final: 0.8534 (mttm) REVERT: B 984 LEU cc_start: 0.8637 (mt) cc_final: 0.8237 (tp) REVERT: B 1041 ASP cc_start: 0.7777 (m-30) cc_final: 0.7365 (m-30) REVERT: B 1045 LYS cc_start: 0.8296 (mmmm) cc_final: 0.7682 (mmmm) REVERT: B 1050 MET cc_start: 0.8705 (ptp) cc_final: 0.8256 (ptp) REVERT: B 1119 ASN cc_start: 0.7276 (m-40) cc_final: 0.6810 (m-40) REVERT: a 85 SER cc_start: 0.7987 (t) cc_final: 0.7542 (p) REVERT: a 106 TRP cc_start: 0.6371 (p90) cc_final: 0.6059 (p90) REVERT: a 153 PHE cc_start: 0.8394 (t80) cc_final: 0.7482 (t80) REVERT: a 154 PRO cc_start: 0.8637 (Cg_endo) cc_final: 0.8341 (Cg_exo) REVERT: b 107 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.5787 (mmmt) REVERT: b 167 TRP cc_start: 0.7863 (p90) cc_final: 0.7624 (p90) outliers start: 117 outliers final: 81 residues processed: 688 average time/residue: 0.4436 time to fit residues: 473.4242 Evaluate side-chains 708 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 617 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 107 LYS Chi-restraints excluded: chain b residue 152 TRP Chi-restraints excluded: chain b residue 182 THR Chi-restraints excluded: chain b residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 10.0000 chunk 41 optimal weight: 0.0000 chunk 208 optimal weight: 2.9990 chunk 267 optimal weight: 0.6980 chunk 206 optimal weight: 0.0770 chunk 307 optimal weight: 0.0570 chunk 204 optimal weight: 2.9990 chunk 364 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.3660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 343 ASN C 409 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30457 Z= 0.154 Angle : 0.554 11.949 41433 Z= 0.280 Chirality : 0.043 0.203 4671 Planarity : 0.004 0.052 5342 Dihedral : 4.420 57.601 4092 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.19 % Allowed : 16.57 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.13), residues: 3749 helix: 1.06 (0.22), residues: 636 sheet: 0.55 (0.17), residues: 862 loop : -0.92 (0.12), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 104 HIS 0.010 0.001 HIS C 245 PHE 0.031 0.001 PHE C 338 TYR 0.036 0.001 TYR C 365 ARG 0.005 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 628 time to evaluate : 3.246 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: A 160 TYR cc_start: 0.7340 (p90) cc_final: 0.6772 (p90) REVERT: A 190 ARG cc_start: 0.7245 (mtt180) cc_final: 0.6773 (mtt180) REVERT: A 206 LYS cc_start: 0.8696 (tmtt) cc_final: 0.8120 (tptp) REVERT: A 221 SER cc_start: 0.8654 (t) cc_final: 0.8257 (p) REVERT: A 564 GLN cc_start: 0.8459 (tt0) cc_final: 0.7890 (mm-40) REVERT: A 574 ASP cc_start: 0.6174 (p0) cc_final: 0.5771 (t0) REVERT: A 655 TYR cc_start: 0.8678 (t80) cc_final: 0.8337 (t80) REVERT: A 740 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7821 (tpp) REVERT: A 752 LEU cc_start: 0.8940 (mt) cc_final: 0.8662 (mt) REVERT: A 779 GLN cc_start: 0.8482 (tp-100) cc_final: 0.7799 (tm-30) REVERT: A 823 PHE cc_start: 0.8342 (t80) cc_final: 0.8080 (t80) REVERT: A 872 GLN cc_start: 0.7677 (tt0) cc_final: 0.7446 (tt0) REVERT: A 900 MET cc_start: 0.8289 (ptp) cc_final: 0.8055 (ptp) REVERT: A 914 ASN cc_start: 0.8342 (m-40) cc_final: 0.7934 (m-40) REVERT: A 935 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8527 (tm-30) REVERT: A 937 SER cc_start: 0.8956 (m) cc_final: 0.8701 (t) REVERT: A 950 ASP cc_start: 0.7105 (t0) cc_final: 0.6567 (t0) REVERT: A 955 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.8150 (t0) REVERT: A 964 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8393 (mmmt) REVERT: A 969 LYS cc_start: 0.9027 (mttt) cc_final: 0.8403 (mmtt) REVERT: A 979 ASP cc_start: 0.7893 (m-30) cc_final: 0.7561 (t0) REVERT: A 984 LEU cc_start: 0.8175 (mt) cc_final: 0.7772 (tp) REVERT: A 985 ASP cc_start: 0.8362 (m-30) cc_final: 0.7913 (p0) REVERT: A 990 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7792 (pp20) REVERT: A 1002 GLN cc_start: 0.7971 (tp40) cc_final: 0.7576 (mm-40) REVERT: A 1110 TYR cc_start: 0.8672 (t80) cc_final: 0.8390 (t80) REVERT: A 1111 GLU cc_start: 0.8404 (tt0) cc_final: 0.8143 (mt-10) REVERT: C 52 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7195 (tm-30) REVERT: C 92 PHE cc_start: 0.7617 (t80) cc_final: 0.7195 (t80) REVERT: C 106 PHE cc_start: 0.7386 (m-80) cc_final: 0.7038 (m-80) REVERT: C 173 GLN cc_start: 0.7013 (pp30) cc_final: 0.6566 (pp30) REVERT: C 189 LEU cc_start: 0.8243 (tp) cc_final: 0.7790 (pp) REVERT: C 220 PHE cc_start: 0.7772 (t80) cc_final: 0.7382 (t80) REVERT: C 237 ARG cc_start: 0.7621 (mtm180) cc_final: 0.7202 (mtm180) REVERT: C 269 TYR cc_start: 0.8043 (m-80) cc_final: 0.7388 (m-80) REVERT: C 289 VAL cc_start: 0.8917 (t) cc_final: 0.8544 (p) REVERT: C 304 LYS cc_start: 0.8902 (mttt) cc_final: 0.8428 (mmmm) REVERT: C 309 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7640 (mt-10) REVERT: C 356 LYS cc_start: 0.8536 (ttpt) cc_final: 0.8218 (ttmt) REVERT: C 389 ASP cc_start: 0.8707 (m-30) cc_final: 0.8421 (p0) REVERT: C 498 ARG cc_start: 0.7140 (tpp80) cc_final: 0.6900 (tpp80) REVERT: C 515 PHE cc_start: 0.7377 (m-80) cc_final: 0.7149 (m-80) REVERT: C 537 LYS cc_start: 0.8618 (tptt) cc_final: 0.7422 (tptm) REVERT: C 613 GLN cc_start: 0.7892 (pt0) cc_final: 0.7611 (pt0) REVERT: C 644 GLN cc_start: 0.7042 (tp-100) cc_final: 0.6733 (tp-100) REVERT: C 741 TYR cc_start: 0.8488 (t80) cc_final: 0.8004 (t80) REVERT: C 745 ASP cc_start: 0.6834 (m-30) cc_final: 0.6568 (t70) REVERT: C 776 LYS cc_start: 0.8360 (ttpp) cc_final: 0.7985 (ttpp) REVERT: C 884 SER cc_start: 0.8695 (m) cc_final: 0.8201 (t) REVERT: C 957 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7602 (tm-30) REVERT: C 969 LYS cc_start: 0.9021 (mttt) cc_final: 0.8683 (mtmm) REVERT: C 979 ASP cc_start: 0.8186 (m-30) cc_final: 0.7637 (m-30) REVERT: C 1002 GLN cc_start: 0.8039 (tp40) cc_final: 0.7582 (tm-30) REVERT: C 1073 LYS cc_start: 0.8212 (mttt) cc_final: 0.7800 (mttm) REVERT: C 1139 ASP cc_start: 0.8280 (t0) cc_final: 0.7928 (t0) REVERT: c 34 MET cc_start: 0.4890 (mmm) cc_final: 0.3964 (mmm) REVERT: B 64 TRP cc_start: 0.6889 (t60) cc_final: 0.6638 (t60) REVERT: B 97 LYS cc_start: 0.5733 (OUTLIER) cc_final: 0.4931 (mmpt) REVERT: B 190 ARG cc_start: 0.4910 (ttt180) cc_final: 0.3925 (ttm170) REVERT: B 203 ILE cc_start: 0.8695 (mt) cc_final: 0.8289 (pt) REVERT: B 206 LYS cc_start: 0.7705 (tppt) cc_final: 0.7494 (tptp) REVERT: B 271 GLN cc_start: 0.8252 (mm110) cc_final: 0.7942 (mm-40) REVERT: B 353 TRP cc_start: 0.5223 (p90) cc_final: 0.4615 (p90) REVERT: B 355 ARG cc_start: 0.8073 (ttt180) cc_final: 0.7316 (tpp80) REVERT: B 508 TYR cc_start: 0.7191 (m-80) cc_final: 0.6902 (m-80) REVERT: B 580 GLN cc_start: 0.8119 (tp40) cc_final: 0.7881 (tp40) REVERT: B 675 GLN cc_start: 0.6784 (mm-40) cc_final: 0.6435 (mm-40) REVERT: B 814 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8266 (mmmt) REVERT: B 868 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7333 (tm-30) REVERT: B 884 SER cc_start: 0.8749 (m) cc_final: 0.8239 (t) REVERT: B 902 MET cc_start: 0.8188 (mmm) cc_final: 0.7361 (mmt) REVERT: B 918 GLU cc_start: 0.8494 (mp0) cc_final: 0.7888 (mp0) REVERT: B 933 LYS cc_start: 0.8399 (mptt) cc_final: 0.8163 (mptt) REVERT: B 936 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7448 (t0) REVERT: B 954 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.8005 (m170) REVERT: B 969 LYS cc_start: 0.9094 (mttt) cc_final: 0.8530 (mttm) REVERT: B 984 LEU cc_start: 0.8633 (mt) cc_final: 0.8222 (tp) REVERT: B 1017 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7956 (tp30) REVERT: B 1045 LYS cc_start: 0.8286 (mmmm) cc_final: 0.7978 (mmmm) REVERT: B 1116 THR cc_start: 0.7587 (m) cc_final: 0.7260 (p) REVERT: B 1119 ASN cc_start: 0.7212 (m-40) cc_final: 0.6691 (m-40) REVERT: a 85 SER cc_start: 0.7968 (t) cc_final: 0.7516 (p) REVERT: a 153 PHE cc_start: 0.8435 (t80) cc_final: 0.7439 (t80) REVERT: a 154 PRO cc_start: 0.8615 (Cg_endo) cc_final: 0.8249 (Cg_exo) REVERT: b 107 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.5705 (mmmt) REVERT: b 167 TRP cc_start: 0.7835 (p90) cc_final: 0.7590 (p90) outliers start: 106 outliers final: 79 residues processed: 675 average time/residue: 0.4635 time to fit residues: 483.1357 Evaluate side-chains 694 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 608 time to evaluate : 3.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 49 LYS Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 107 LYS Chi-restraints excluded: chain b residue 152 TRP Chi-restraints excluded: chain b residue 182 THR Chi-restraints excluded: chain b residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 109 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 231 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 180 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 286 optimal weight: 0.0770 overall best weight: 1.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 245 HIS C 481 ASN C 544 ASN C 658 ASN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.7195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 30457 Z= 0.306 Angle : 0.627 10.305 41433 Z= 0.323 Chirality : 0.045 0.202 4671 Planarity : 0.004 0.062 5342 Dihedral : 4.685 57.294 4092 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.62 % Allowed : 16.51 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.13), residues: 3749 helix: 0.80 (0.22), residues: 651 sheet: 0.38 (0.16), residues: 931 loop : -1.00 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 104 HIS 0.010 0.002 HIS C 207 PHE 0.029 0.002 PHE B 329 TYR 0.022 0.001 TYR C 365 ARG 0.011 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 640 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7813 (m) cc_final: 0.7490 (p) REVERT: A 138 ASP cc_start: 0.8373 (t0) cc_final: 0.8103 (t0) REVERT: A 160 TYR cc_start: 0.7521 (p90) cc_final: 0.7124 (p90) REVERT: A 206 LYS cc_start: 0.8768 (tmtt) cc_final: 0.8168 (tptp) REVERT: A 221 SER cc_start: 0.8689 (t) cc_final: 0.8228 (p) REVERT: A 298 GLU cc_start: 0.8339 (tp30) cc_final: 0.8102 (tp30) REVERT: A 606 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8557 (t0) REVERT: A 655 TYR cc_start: 0.8757 (t80) cc_final: 0.8442 (t80) REVERT: A 740 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7960 (tpp) REVERT: A 779 GLN cc_start: 0.8468 (tp-100) cc_final: 0.7733 (tm-30) REVERT: A 823 PHE cc_start: 0.8363 (t80) cc_final: 0.8013 (t80) REVERT: A 872 GLN cc_start: 0.7791 (tt0) cc_final: 0.7521 (tt0) REVERT: A 914 ASN cc_start: 0.8381 (m-40) cc_final: 0.7906 (m-40) REVERT: A 935 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8476 (tm-30) REVERT: A 937 SER cc_start: 0.9024 (m) cc_final: 0.8761 (t) REVERT: A 950 ASP cc_start: 0.7208 (t0) cc_final: 0.6684 (t0) REVERT: A 955 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8252 (t0) REVERT: A 964 LYS cc_start: 0.8856 (mmmm) cc_final: 0.8502 (mmmt) REVERT: A 969 LYS cc_start: 0.9008 (mttt) cc_final: 0.8355 (mmtt) REVERT: A 979 ASP cc_start: 0.8026 (m-30) cc_final: 0.7707 (t0) REVERT: A 984 LEU cc_start: 0.8162 (mt) cc_final: 0.7701 (tp) REVERT: A 985 ASP cc_start: 0.8476 (m-30) cc_final: 0.7727 (p0) REVERT: A 990 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7851 (pp20) REVERT: A 1002 GLN cc_start: 0.8065 (tp40) cc_final: 0.7636 (mm-40) REVERT: A 1045 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8237 (tptp) REVERT: C 52 GLN cc_start: 0.7850 (tm-30) cc_final: 0.7384 (tm-30) REVERT: C 92 PHE cc_start: 0.7672 (t80) cc_final: 0.7193 (t80) REVERT: C 106 PHE cc_start: 0.7379 (m-80) cc_final: 0.7077 (m-80) REVERT: C 201 PHE cc_start: 0.8530 (t80) cc_final: 0.8212 (t80) REVERT: C 220 PHE cc_start: 0.7820 (t80) cc_final: 0.7483 (t80) REVERT: C 237 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7388 (mtm180) REVERT: C 240 THR cc_start: 0.8154 (m) cc_final: 0.7422 (t) REVERT: C 269 TYR cc_start: 0.8050 (m-80) cc_final: 0.7283 (m-10) REVERT: C 289 VAL cc_start: 0.8931 (t) cc_final: 0.8564 (p) REVERT: C 298 GLU cc_start: 0.8327 (tp30) cc_final: 0.7938 (tp30) REVERT: C 304 LYS cc_start: 0.8898 (mttt) cc_final: 0.8535 (mmmm) REVERT: C 309 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7741 (mt-10) REVERT: C 498 ARG cc_start: 0.7453 (tpp80) cc_final: 0.7165 (tpp80) REVERT: C 537 LYS cc_start: 0.8546 (tptt) cc_final: 0.7834 (tptp) REVERT: C 644 GLN cc_start: 0.6957 (tp-100) cc_final: 0.6643 (tp-100) REVERT: C 710 ASN cc_start: 0.8235 (m110) cc_final: 0.7812 (p0) REVERT: C 739 THR cc_start: 0.7490 (m) cc_final: 0.7012 (p) REVERT: C 775 ASP cc_start: 0.8176 (t0) cc_final: 0.7505 (t0) REVERT: C 776 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7953 (ttpp) REVERT: C 814 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8269 (mmmt) REVERT: C 884 SER cc_start: 0.8767 (m) cc_final: 0.8279 (t) REVERT: C 918 GLU cc_start: 0.7964 (mp0) cc_final: 0.7271 (mp0) REVERT: C 921 LYS cc_start: 0.8904 (mttt) cc_final: 0.8573 (mttt) REVERT: C 969 LYS cc_start: 0.9075 (mttt) cc_final: 0.8749 (mtmm) REVERT: C 1002 GLN cc_start: 0.8207 (tp40) cc_final: 0.7665 (tm-30) REVERT: C 1073 LYS cc_start: 0.8327 (mttt) cc_final: 0.7909 (mttm) REVERT: C 1139 ASP cc_start: 0.8446 (t0) cc_final: 0.8178 (t0) REVERT: c 34 MET cc_start: 0.4913 (mmm) cc_final: 0.3992 (mmm) REVERT: B 190 ARG cc_start: 0.4703 (ttt180) cc_final: 0.3625 (ttm170) REVERT: B 206 LYS cc_start: 0.7887 (tppt) cc_final: 0.7639 (tptp) REVERT: B 351 TYR cc_start: 0.8516 (p90) cc_final: 0.7909 (p90) REVERT: B 355 ARG cc_start: 0.8108 (ttt180) cc_final: 0.7380 (tpp80) REVERT: B 508 TYR cc_start: 0.7299 (m-80) cc_final: 0.7024 (m-80) REVERT: B 675 GLN cc_start: 0.6840 (mm-40) cc_final: 0.6461 (mm-40) REVERT: B 868 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7526 (tm-30) REVERT: B 884 SER cc_start: 0.8864 (m) cc_final: 0.8354 (t) REVERT: B 935 GLN cc_start: 0.7896 (tt0) cc_final: 0.7612 (tm-30) REVERT: B 969 LYS cc_start: 0.9142 (mttt) cc_final: 0.8571 (mttm) REVERT: B 984 LEU cc_start: 0.8676 (mt) cc_final: 0.8235 (tp) REVERT: B 988 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8245 (mm-30) REVERT: B 1045 LYS cc_start: 0.8347 (mmmm) cc_final: 0.8046 (mmmm) REVERT: B 1074 ASN cc_start: 0.7836 (m-40) cc_final: 0.7553 (m110) REVERT: B 1116 THR cc_start: 0.7705 (m) cc_final: 0.7348 (p) REVERT: B 1119 ASN cc_start: 0.7437 (m-40) cc_final: 0.6976 (m-40) REVERT: a 36 TRP cc_start: 0.7716 (m100) cc_final: 0.7171 (m100) REVERT: a 85 SER cc_start: 0.7953 (t) cc_final: 0.7496 (p) REVERT: a 153 PHE cc_start: 0.8536 (t80) cc_final: 0.7461 (t80) REVERT: a 154 PRO cc_start: 0.8794 (Cg_endo) cc_final: 0.8468 (Cg_exo) REVERT: b 41 GLN cc_start: 0.8344 (tt0) cc_final: 0.8138 (tp40) REVERT: b 167 TRP cc_start: 0.7925 (p90) cc_final: 0.7565 (p90) REVERT: b 170 GLN cc_start: 0.8242 (tp40) cc_final: 0.8001 (tp40) REVERT: b 196 TYR cc_start: 0.7544 (m-10) cc_final: 0.7263 (m-10) outliers start: 120 outliers final: 88 residues processed: 693 average time/residue: 0.4514 time to fit residues: 482.4858 Evaluate side-chains 720 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 628 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 152 TRP Chi-restraints excluded: chain b residue 182 THR Chi-restraints excluded: chain b residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 0.6980 chunk 349 optimal weight: 5.9990 chunk 318 optimal weight: 0.9990 chunk 339 optimal weight: 2.9990 chunk 348 optimal weight: 6.9990 chunk 204 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 306 optimal weight: 0.7980 chunk 321 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN C 49 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 762 GLN C 901 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 128 GLN ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.7306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30457 Z= 0.195 Angle : 0.585 10.674 41433 Z= 0.298 Chirality : 0.044 0.184 4671 Planarity : 0.004 0.056 5342 Dihedral : 4.576 55.611 4092 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.77 % Allowed : 17.99 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 3749 helix: 1.03 (0.22), residues: 651 sheet: 0.38 (0.16), residues: 933 loop : -0.99 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 104 HIS 0.032 0.001 HIS C 207 PHE 0.029 0.001 PHE B 329 TYR 0.018 0.001 TYR a 129 ARG 0.006 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 637 time to evaluate : 3.277 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: A 138 ASP cc_start: 0.8276 (t0) cc_final: 0.8075 (t0) REVERT: A 160 TYR cc_start: 0.7511 (p90) cc_final: 0.7064 (p90) REVERT: A 190 ARG cc_start: 0.7648 (mtt180) cc_final: 0.7082 (mtt180) REVERT: A 206 LYS cc_start: 0.8708 (tmtt) cc_final: 0.8110 (tptp) REVERT: A 221 SER cc_start: 0.8643 (t) cc_final: 0.8192 (p) REVERT: A 655 TYR cc_start: 0.8721 (t80) cc_final: 0.8370 (t80) REVERT: A 710 ASN cc_start: 0.7861 (p0) cc_final: 0.7417 (p0) REVERT: A 740 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7866 (tpp) REVERT: A 779 GLN cc_start: 0.8446 (tp-100) cc_final: 0.7758 (tm-30) REVERT: A 823 PHE cc_start: 0.8310 (t80) cc_final: 0.7980 (t80) REVERT: A 872 GLN cc_start: 0.7738 (tt0) cc_final: 0.7480 (tt0) REVERT: A 914 ASN cc_start: 0.8276 (m-40) cc_final: 0.7930 (m-40) REVERT: A 933 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8192 (mmmm) REVERT: A 935 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8624 (tm-30) REVERT: A 937 SER cc_start: 0.9003 (m) cc_final: 0.8763 (t) REVERT: A 950 ASP cc_start: 0.7148 (t0) cc_final: 0.6852 (t0) REVERT: A 955 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.8181 (t0) REVERT: A 964 LYS cc_start: 0.8842 (mmmm) cc_final: 0.8443 (mmmt) REVERT: A 969 LYS cc_start: 0.8973 (mttt) cc_final: 0.8276 (mmtt) REVERT: A 979 ASP cc_start: 0.7912 (m-30) cc_final: 0.7671 (t0) REVERT: A 984 LEU cc_start: 0.8142 (mt) cc_final: 0.7746 (tp) REVERT: A 985 ASP cc_start: 0.8413 (m-30) cc_final: 0.7875 (p0) REVERT: A 1002 GLN cc_start: 0.7990 (tp40) cc_final: 0.7602 (mm-40) REVERT: A 1045 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8225 (tptp) REVERT: A 1084 ASP cc_start: 0.8183 (p0) cc_final: 0.7916 (p0) REVERT: C 52 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7377 (tm-30) REVERT: C 92 PHE cc_start: 0.7645 (t80) cc_final: 0.7161 (t80) REVERT: C 106 PHE cc_start: 0.7476 (m-80) cc_final: 0.7172 (m-80) REVERT: C 121 ASN cc_start: 0.8716 (m110) cc_final: 0.7934 (p0) REVERT: C 173 GLN cc_start: 0.7136 (pp30) cc_final: 0.6576 (pp30) REVERT: C 201 PHE cc_start: 0.8470 (t80) cc_final: 0.8268 (t80) REVERT: C 220 PHE cc_start: 0.7710 (t80) cc_final: 0.7393 (t80) REVERT: C 237 ARG cc_start: 0.7658 (mtm180) cc_final: 0.7280 (mtm180) REVERT: C 240 THR cc_start: 0.8092 (m) cc_final: 0.7393 (t) REVERT: C 269 TYR cc_start: 0.8230 (m-80) cc_final: 0.7493 (m-10) REVERT: C 289 VAL cc_start: 0.8933 (t) cc_final: 0.8554 (p) REVERT: C 298 GLU cc_start: 0.8286 (tp30) cc_final: 0.7588 (tp30) REVERT: C 304 LYS cc_start: 0.8888 (mttt) cc_final: 0.8512 (mmmm) REVERT: C 309 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7756 (mt-10) REVERT: C 356 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8267 (ttmt) REVERT: C 389 ASP cc_start: 0.8709 (m-30) cc_final: 0.8325 (p0) REVERT: C 498 ARG cc_start: 0.7457 (tpp80) cc_final: 0.7171 (tpp80) REVERT: C 529 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7713 (tppp) REVERT: C 537 LYS cc_start: 0.8639 (tptt) cc_final: 0.7860 (tptp) REVERT: C 644 GLN cc_start: 0.6982 (tp-100) cc_final: 0.6652 (tp-100) REVERT: C 675 GLN cc_start: 0.7436 (pp30) cc_final: 0.7157 (tm-30) REVERT: C 710 ASN cc_start: 0.8180 (m110) cc_final: 0.7777 (p0) REVERT: C 739 THR cc_start: 0.7398 (m) cc_final: 0.6773 (p) REVERT: C 775 ASP cc_start: 0.8170 (t0) cc_final: 0.7561 (t0) REVERT: C 776 LYS cc_start: 0.8307 (ttpp) cc_final: 0.7989 (ttpp) REVERT: C 814 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8327 (mmmt) REVERT: C 884 SER cc_start: 0.8770 (m) cc_final: 0.8261 (t) REVERT: C 918 GLU cc_start: 0.8031 (mp0) cc_final: 0.7304 (mp0) REVERT: C 921 LYS cc_start: 0.8914 (mttt) cc_final: 0.8574 (mttt) REVERT: C 969 LYS cc_start: 0.9070 (mttt) cc_final: 0.8725 (mtmm) REVERT: C 1002 GLN cc_start: 0.8066 (tp40) cc_final: 0.7585 (tm-30) REVERT: C 1073 LYS cc_start: 0.8209 (mttt) cc_final: 0.7809 (mttm) REVERT: C 1139 ASP cc_start: 0.8417 (t0) cc_final: 0.8128 (t0) REVERT: c 34 MET cc_start: 0.4874 (mmm) cc_final: 0.3960 (mmm) REVERT: B 190 ARG cc_start: 0.4659 (ttt180) cc_final: 0.3476 (ttm170) REVERT: B 206 LYS cc_start: 0.7819 (tppt) cc_final: 0.7536 (tptp) REVERT: B 271 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7973 (mm-40) REVERT: B 389 ASP cc_start: 0.7903 (p0) cc_final: 0.7610 (p0) REVERT: B 508 TYR cc_start: 0.7390 (m-80) cc_final: 0.7114 (m-80) REVERT: B 529 LYS cc_start: 0.8099 (tppt) cc_final: 0.7842 (tppt) REVERT: B 562 PHE cc_start: 0.7126 (m-10) cc_final: 0.6827 (m-10) REVERT: B 580 GLN cc_start: 0.8284 (tp40) cc_final: 0.7935 (tp40) REVERT: B 675 GLN cc_start: 0.6792 (mm-40) cc_final: 0.6427 (mm-40) REVERT: B 868 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7371 (tm-30) REVERT: B 884 SER cc_start: 0.8890 (m) cc_final: 0.8379 (t) REVERT: B 954 HIS cc_start: 0.8362 (m90) cc_final: 0.8043 (m170) REVERT: B 969 LYS cc_start: 0.9102 (mttt) cc_final: 0.8571 (mttm) REVERT: B 984 LEU cc_start: 0.8660 (mt) cc_final: 0.8244 (tp) REVERT: B 988 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8307 (mm-30) REVERT: B 1041 ASP cc_start: 0.7860 (m-30) cc_final: 0.7390 (m-30) REVERT: B 1045 LYS cc_start: 0.8321 (mmmm) cc_final: 0.7700 (mmmm) REVERT: B 1116 THR cc_start: 0.7621 (m) cc_final: 0.7280 (p) REVERT: B 1119 ASN cc_start: 0.7351 (m-40) cc_final: 0.6896 (m-40) REVERT: a 85 SER cc_start: 0.7942 (t) cc_final: 0.7471 (p) REVERT: a 153 PHE cc_start: 0.8574 (t80) cc_final: 0.7529 (t80) REVERT: a 154 PRO cc_start: 0.8698 (Cg_endo) cc_final: 0.8358 (Cg_exo) REVERT: b 167 TRP cc_start: 0.7887 (p90) cc_final: 0.7613 (p90) REVERT: b 196 TYR cc_start: 0.7710 (m-10) cc_final: 0.7460 (m-10) outliers start: 92 outliers final: 73 residues processed: 678 average time/residue: 0.4326 time to fit residues: 455.2506 Evaluate side-chains 694 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 617 time to evaluate : 3.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 152 TRP Chi-restraints excluded: chain b residue 182 THR Chi-restraints excluded: chain b residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 359 optimal weight: 9.9990 chunk 219 optimal weight: 20.0000 chunk 170 optimal weight: 1.9990 chunk 249 optimal weight: 0.8980 chunk 376 optimal weight: 10.0000 chunk 346 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 231 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN C 245 HIS C 564 GLN C 762 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C 935 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 613 GLN B 710 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN ** a 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 128 GLN ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.8150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.096 30457 Z= 0.601 Angle : 0.855 10.704 41433 Z= 0.452 Chirality : 0.053 0.342 4671 Planarity : 0.006 0.151 5342 Dihedral : 5.658 46.812 4092 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 3.37 % Allowed : 17.84 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -1.20 (0.13), residues: 3749 helix: -0.03 (0.20), residues: 667 sheet: -0.01 (0.16), residues: 966 loop : -1.47 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 104 HIS 0.015 0.003 HIS B1064 PHE 0.045 0.003 PHE B 490 TYR 0.033 0.003 TYR C 508 ARG 0.016 0.001 ARG B 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 640 time to evaluate : 3.618 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: A 86 PHE cc_start: 0.7539 (t80) cc_final: 0.7287 (t80) REVERT: A 160 TYR cc_start: 0.7954 (p90) cc_final: 0.7438 (p90) REVERT: A 177 MET cc_start: -0.4028 (OUTLIER) cc_final: -0.4372 (mtt) REVERT: A 190 ARG cc_start: 0.7715 (mtt180) cc_final: 0.6864 (mtt180) REVERT: A 206 LYS cc_start: 0.8846 (tmtt) cc_final: 0.8194 (tptp) REVERT: A 221 SER cc_start: 0.8766 (t) cc_final: 0.8321 (p) REVERT: A 298 GLU cc_start: 0.8447 (tp30) cc_final: 0.8034 (tt0) REVERT: A 314 GLN cc_start: 0.7160 (tm-30) cc_final: 0.6703 (tm-30) REVERT: A 606 ASN cc_start: 0.9035 (OUTLIER) cc_final: 0.8486 (t0) REVERT: A 655 TYR cc_start: 0.8815 (t80) cc_final: 0.8464 (t80) REVERT: A 740 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8115 (ttt) REVERT: A 786 LYS cc_start: 0.8256 (mttt) cc_final: 0.8042 (mttt) REVERT: A 823 PHE cc_start: 0.8588 (t80) cc_final: 0.8240 (t80) REVERT: A 914 ASN cc_start: 0.8354 (m-40) cc_final: 0.8083 (m-40) REVERT: A 935 GLN cc_start: 0.9225 (tm-30) cc_final: 0.8628 (tm-30) REVERT: A 937 SER cc_start: 0.9048 (m) cc_final: 0.8764 (t) REVERT: A 950 ASP cc_start: 0.7249 (t0) cc_final: 0.6952 (t0) REVERT: A 955 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8296 (t0) REVERT: A 969 LYS cc_start: 0.9046 (mttt) cc_final: 0.8268 (mtpp) REVERT: A 979 ASP cc_start: 0.8029 (m-30) cc_final: 0.7767 (t0) REVERT: A 984 LEU cc_start: 0.8330 (mt) cc_final: 0.7779 (tp) REVERT: A 985 ASP cc_start: 0.8625 (m-30) cc_final: 0.8001 (p0) REVERT: A 990 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7905 (pp20) REVERT: A 1045 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8325 (tptp) REVERT: A 1072 GLU cc_start: 0.8416 (pm20) cc_final: 0.8096 (mp0) REVERT: A 1084 ASP cc_start: 0.8440 (p0) cc_final: 0.8227 (p0) REVERT: C 52 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7778 (tm-30) REVERT: C 92 PHE cc_start: 0.7721 (t80) cc_final: 0.7321 (t80) REVERT: C 106 PHE cc_start: 0.7514 (m-80) cc_final: 0.7217 (m-80) REVERT: C 121 ASN cc_start: 0.8805 (m110) cc_final: 0.7962 (p0) REVERT: C 173 GLN cc_start: 0.7447 (pp30) cc_final: 0.7198 (pp30) REVERT: C 189 LEU cc_start: 0.8483 (tp) cc_final: 0.7812 (pp) REVERT: C 201 PHE cc_start: 0.8554 (t80) cc_final: 0.8271 (t80) REVERT: C 237 ARG cc_start: 0.7657 (mtm180) cc_final: 0.7371 (mtm180) REVERT: C 289 VAL cc_start: 0.8928 (t) cc_final: 0.8578 (p) REVERT: C 298 GLU cc_start: 0.8410 (tp30) cc_final: 0.8028 (tp30) REVERT: C 304 LYS cc_start: 0.8994 (mttt) cc_final: 0.8652 (mmmm) REVERT: C 309 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7844 (mt-10) REVERT: C 356 LYS cc_start: 0.8619 (ttmt) cc_final: 0.8275 (ttmt) REVERT: C 387 LEU cc_start: 0.8654 (mt) cc_final: 0.8226 (mt) REVERT: C 450 ASN cc_start: 0.7704 (m-40) cc_final: 0.7402 (t0) REVERT: C 498 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7792 (tpp80) REVERT: C 529 LYS cc_start: 0.8426 (tppp) cc_final: 0.8141 (mmmt) REVERT: C 537 LYS cc_start: 0.8588 (tptt) cc_final: 0.8211 (tptp) REVERT: C 613 GLN cc_start: 0.8216 (pt0) cc_final: 0.7889 (pt0) REVERT: C 644 GLN cc_start: 0.6887 (tp-100) cc_final: 0.6602 (tp-100) REVERT: C 707 TYR cc_start: 0.4940 (m-80) cc_final: 0.4174 (m-80) REVERT: C 710 ASN cc_start: 0.8317 (m110) cc_final: 0.7955 (p0) REVERT: C 753 LEU cc_start: 0.9524 (tp) cc_final: 0.9249 (tp) REVERT: C 768 THR cc_start: 0.8682 (m) cc_final: 0.8377 (t) REVERT: C 775 ASP cc_start: 0.8264 (t0) cc_final: 0.7548 (t0) REVERT: C 814 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8336 (mmmt) REVERT: C 884 SER cc_start: 0.8859 (m) cc_final: 0.8344 (t) REVERT: C 918 GLU cc_start: 0.7924 (mp0) cc_final: 0.7501 (mp0) REVERT: C 921 LYS cc_start: 0.9005 (mttt) cc_final: 0.8658 (mttt) REVERT: C 957 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7978 (tm-30) REVERT: C 969 LYS cc_start: 0.9131 (mttt) cc_final: 0.8807 (mtpp) REVERT: C 1002 GLN cc_start: 0.8464 (tp40) cc_final: 0.7671 (tm-30) REVERT: C 1073 LYS cc_start: 0.8425 (mttt) cc_final: 0.8008 (mttm) REVERT: C 1129 VAL cc_start: 0.8941 (t) cc_final: 0.8705 (m) REVERT: C 1139 ASP cc_start: 0.8747 (t0) cc_final: 0.8404 (t0) REVERT: B 195 LYS cc_start: 0.7444 (tptt) cc_final: 0.7172 (tppt) REVERT: B 206 LYS cc_start: 0.8244 (tppt) cc_final: 0.7961 (tptp) REVERT: B 224 GLU cc_start: 0.6623 (mm-30) cc_final: 0.6328 (mp0) REVERT: B 237 ARG cc_start: 0.6942 (ttp-110) cc_final: 0.6466 (mtp85) REVERT: B 266 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.7064 (p90) REVERT: B 271 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8035 (mm-40) REVERT: B 355 ARG cc_start: 0.8278 (ttt180) cc_final: 0.8012 (ttt180) REVERT: B 380 TYR cc_start: 0.7778 (m-10) cc_final: 0.7158 (m-10) REVERT: B 389 ASP cc_start: 0.7933 (p0) cc_final: 0.7638 (p0) REVERT: B 556 ASN cc_start: 0.8444 (p0) cc_final: 0.7760 (t0) REVERT: B 562 PHE cc_start: 0.7822 (m-10) cc_final: 0.7281 (m-10) REVERT: B 661 GLU cc_start: 0.7838 (tt0) cc_final: 0.7573 (tt0) REVERT: B 675 GLN cc_start: 0.6928 (mm-40) cc_final: 0.6571 (mm-40) REVERT: B 698 SER cc_start: 0.8393 (p) cc_final: 0.8187 (p) REVERT: B 765 ARG cc_start: 0.8533 (tmm-80) cc_final: 0.8328 (ttp80) REVERT: B 787 GLN cc_start: 0.8416 (mp10) cc_final: 0.8195 (mp10) REVERT: B 868 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7480 (tm-30) REVERT: B 884 SER cc_start: 0.8976 (m) cc_final: 0.8376 (t) REVERT: B 969 LYS cc_start: 0.9217 (mttt) cc_final: 0.8705 (mttm) REVERT: B 984 LEU cc_start: 0.8691 (mt) cc_final: 0.8466 (mm) REVERT: B 1041 ASP cc_start: 0.8029 (m-30) cc_final: 0.7572 (m-30) REVERT: B 1045 LYS cc_start: 0.8471 (mmmm) cc_final: 0.7841 (mmmm) REVERT: B 1100 THR cc_start: 0.9013 (m) cc_final: 0.8699 (p) REVERT: B 1116 THR cc_start: 0.7821 (m) cc_final: 0.7438 (p) REVERT: B 1119 ASN cc_start: 0.7554 (m-40) cc_final: 0.6944 (m110) REVERT: a 27 TYR cc_start: 0.7993 (t80) cc_final: 0.7454 (t80) REVERT: a 153 PHE cc_start: 0.8729 (t80) cc_final: 0.8017 (t80) REVERT: b 41 GLN cc_start: 0.8480 (tt0) cc_final: 0.8273 (tp40) REVERT: b 167 TRP cc_start: 0.8001 (p90) cc_final: 0.7784 (p90) REVERT: b 196 TYR cc_start: 0.7663 (m-10) cc_final: 0.7402 (m-10) outliers start: 112 outliers final: 86 residues processed: 688 average time/residue: 0.4423 time to fit residues: 471.2476 Evaluate side-chains 700 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 607 time to evaluate : 3.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain a residue 202 CYS Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 152 TRP Chi-restraints excluded: chain b residue 182 THR Chi-restraints excluded: chain b residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 0.4980 chunk 238 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 276 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 83 optimal weight: 0.6980 chunk 300 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 308 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 935 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 613 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 203 ASN ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.170648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131310 restraints weight = 67648.865| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 4.00 r_work: 0.3576 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.8113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30457 Z= 0.217 Angle : 0.653 11.588 41433 Z= 0.333 Chirality : 0.046 0.219 4671 Planarity : 0.004 0.077 5342 Dihedral : 5.024 40.169 4088 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.75 % Rotamer: Outliers : 2.20 % Allowed : 20.01 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.13), residues: 3749 helix: 0.53 (0.21), residues: 679 sheet: 0.12 (0.16), residues: 925 loop : -1.27 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 436 HIS 0.009 0.001 HIS C 207 PHE 0.028 0.002 PHE B 201 TYR 0.020 0.001 TYR A1110 ARG 0.009 0.001 ARG B 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8900.06 seconds wall clock time: 159 minutes 24.79 seconds (9564.79 seconds total)