Starting phenix.real_space_refine on Thu Mar 21 13:13:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxd_32176/03_2024/7vxd_32176.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxd_32176/03_2024/7vxd_32176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxd_32176/03_2024/7vxd_32176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxd_32176/03_2024/7vxd_32176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxd_32176/03_2024/7vxd_32176.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxd_32176/03_2024/7vxd_32176.pdb" } resolution = 4.0 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= 0.005 sd= 0.113 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 146 5.16 5 C 19291 2.51 5 N 5028 2.21 5 O 5729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30194 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8453 Classifications: {'peptide': 1079} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 8423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8423 Classifications: {'peptide': 1075} Link IDs: {'PTRANS': 52, 'TRANS': 1022} Chain breaks: 5 Chain: "C" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "B" Number of atoms: 8448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8448 Classifications: {'peptide': 1078} Link IDs: {'PTRANS': 52, 'TRANS': 1025} Chain breaks: 5 Time building chain proxies: 15.37, per 1000 atoms: 0.51 Number of scatterers: 30194 At special positions: 0 Unit cell: (161.764, 148.648, 262.32, 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 146 16.00 O 5729 8.00 N 5028 7.00 C 19291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, 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=1.90 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 D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 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 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 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: 11.01 Conformation dependent library (CDL) restraints added in 5.2 seconds 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7178 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 47 sheets defined 30.3% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.563A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.948A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.760A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.738A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 780 removed outlier: 3.548A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 removed outlier: 4.349A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.523A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.602A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.138A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.626A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.947A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.509A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.525A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1152 removed outlier: 4.080A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1156 removed outlier: 4.032A pdb=" N PHE A1156 " --> pdb=" O ASP A1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1153 through 1156' Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.530A pdb=" N THR D 299 " --> pdb=" O PRO D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 4.116A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 502 through 506 Processing helix chain 'D' and resid 747 through 755 removed outlier: 3.692A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 780 removed outlier: 3.603A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 825 removed outlier: 3.534A pdb=" N LEU D 822 " --> pdb=" O ILE D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 854 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 897 through 909 removed outlier: 3.760A pdb=" N MET D 902 " --> pdb=" O PHE D 898 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 941 removed outlier: 3.908A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 918 " --> pdb=" O ASN D 914 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.698A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 963 " --> pdb=" O LEU D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 982 removed outlier: 3.697A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.081A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1154 removed outlier: 4.244A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS D1154 " --> pdb=" O GLU D1150 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 53 removed outlier: 4.033A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 removed outlier: 3.768A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.942A pdb=" N GLU C 87 " --> pdb=" O PRO C 84 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 88 " --> pdb=" O LEU C 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 84 through 88' Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.520A pdb=" N LYS C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.971A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 removed outlier: 3.846A pdb=" N ASN C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 155 removed outlier: 3.771A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.613A pdb=" N ARG C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 194 removed outlier: 3.643A pdb=" N MET C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.529A pdb=" N TYR C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP C 203 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 220 through 249 removed outlier: 3.988A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU C 232 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.780A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 293 through 301 removed outlier: 3.781A pdb=" N ASP C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 318 removed outlier: 4.025A pdb=" N PHE C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.634A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 385 removed outlier: 3.644A pdb=" N PHE C 369 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 370 " --> pdb=" O MET C 366 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA C 384 " --> pdb=" O GLN C 380 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 389 through 393 Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.552A pdb=" N VAL C 404 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 412 " --> pdb=" O MET C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.730A pdb=" N ILE C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 447 removed outlier: 3.658A pdb=" N ASN C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 466 removed outlier: 4.002A pdb=" N PHE C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 471 No H-bonds generated for 'chain 'C' and resid 469 through 471' Processing helix chain 'C' and resid 472 through 485 removed outlier: 3.898A pdb=" N GLU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 503 removed outlier: 4.123A pdb=" N SER C 502 " --> pdb=" O CYS C 498 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 503 " --> pdb=" O ASP C 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 498 through 503' Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 513 through 533 removed outlier: 3.529A pdb=" N THR C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS C 530 " --> pdb=" O GLN C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.659A pdb=" N GLN C 552 " --> pdb=" O THR C 548 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN C 556 " --> pdb=" O GLN C 552 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 575 removed outlier: 3.515A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL C 573 " --> pdb=" O ALA C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.575A pdb=" N PHE C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.692A pdb=" N TRP C 594 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.098A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.853A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.973A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.861A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.519A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.962A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 854 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.526A pdb=" N LEU B 877 " --> pdb=" O TYR B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.619A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.818A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.781A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (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 965 removed outlier: 3.764A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.525A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.311A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1152 Processing helix chain 'B' and resid 1154 through 1158 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.761A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.326A 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: 4.418A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.834A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.852A pdb=" N GLY A 142 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 3.521A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 removed outlier: 4.020A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 566 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.743A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 653 through 655 removed outlier: 5.579A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 672 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.552A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.650A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.775A 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 1120 through 1122 removed outlier: 3.600A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 27 through 30 removed outlier: 3.739A pdb=" N ALA D 27 " --> pdb=" O TRP D 64 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR D 265 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 90 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE D 194 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 193 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 227 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.655A pdb=" N THR D 51 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE D 275 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.925A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 107 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS D 131 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLU D 132 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N CYS D 166 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AC2, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.804A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 324 through 327 removed outlier: 6.999A pdb=" N GLU D 324 " --> pdb=" O ASN D 540 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ASN D 542 " --> pdb=" O GLU D 324 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE D 326 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE D 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 354 through 357 removed outlier: 4.324A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 434 " --> pdb=" O VAL D 511 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU D 513 " --> pdb=" O CYS D 432 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS D 432 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 378 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA D 435 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR D 376 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.151A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 701 through 702 removed outlier: 7.268A pdb=" N VAL D 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.584A pdb=" N ILE D 714 " --> pdb=" O LYS D1073 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.668A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.357A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 1120 through 1122 removed outlier: 3.756A pdb=" N ILE D1081 " --> pdb=" O HIS D1088 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.554A pdb=" N LEU C 142 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.126A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 347 through 352 removed outlier: 3.571A pdb=" N THR C 347 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 28 through 31 removed outlier: 8.128A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 28 through 31 removed outlier: 8.128A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 48 through 52 removed outlier: 4.483A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.506A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.358A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.525A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 334 through 335 removed outlier: 7.531A pdb=" N ASN B 334 " --> pdb=" O VAL B 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 357 through 359 removed outlier: 3.988A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.509A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.633A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.580A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.463A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) 1069 hydrogen bonds defined for protein. 3006 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: 12.56 Time building geometry restraints manager: 12.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9747 1.35 - 1.46: 7631 1.46 - 1.58: 13349 1.58 - 1.70: 0 1.70 - 1.82: 197 Bond restraints: 30924 Sorted by residual: bond pdb=" C GLN B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 1.334 1.567 -0.233 2.34e-02 1.83e+03 9.91e+01 bond pdb=" C THR B 478 " pdb=" N PRO B 479 " ideal model delta sigma weight residual 1.334 1.461 -0.127 2.34e-02 1.83e+03 2.96e+01 bond pdb=" C PRO D 25 " pdb=" N PRO D 26 " ideal model delta sigma weight residual 1.334 1.435 -0.101 2.34e-02 1.83e+03 1.87e+01 bond pdb=" C CYS D 336 " pdb=" N PRO D 337 " ideal model delta sigma weight residual 1.334 1.427 -0.094 2.34e-02 1.83e+03 1.60e+01 bond pdb=" C PRO B 25 " pdb=" N PRO B 26 " ideal model delta sigma weight residual 1.334 1.427 -0.093 2.34e-02 1.83e+03 1.57e+01 ... (remaining 30919 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.19: 958 107.19 - 113.90: 16973 113.90 - 120.60: 12218 120.60 - 127.31: 11599 127.31 - 134.01: 305 Bond angle restraints: 42053 Sorted by residual: angle pdb=" N VAL D 362 " pdb=" CA VAL D 362 " pdb=" C VAL D 362 " ideal model delta sigma weight residual 110.72 104.52 6.20 1.01e+00 9.80e-01 3.77e+01 angle pdb=" O ASN D 360 " pdb=" C ASN D 360 " pdb=" N CYS D 361 " ideal model delta sigma weight residual 122.59 129.55 -6.96 1.33e+00 5.65e-01 2.74e+01 angle pdb=" C ASN D 360 " pdb=" N CYS D 361 " pdb=" CA CYS D 361 " ideal model delta sigma weight residual 121.54 130.38 -8.84 1.91e+00 2.74e-01 2.14e+01 angle pdb=" CA ASN D 360 " pdb=" C ASN D 360 " pdb=" N CYS D 361 " ideal model delta sigma weight residual 116.84 109.03 7.81 1.71e+00 3.42e-01 2.09e+01 angle pdb=" C VAL D 362 " pdb=" N ALA D 363 " pdb=" CA ALA D 363 " ideal model delta sigma weight residual 121.54 129.47 -7.93 1.91e+00 2.74e-01 1.73e+01 ... (remaining 42048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 17931 16.01 - 32.02: 302 32.02 - 48.04: 99 48.04 - 64.05: 35 64.05 - 80.06: 12 Dihedral angle restraints: 18379 sinusoidal: 7219 harmonic: 11160 Sorted by residual: dihedral pdb=" CA THR D 531 " pdb=" C THR D 531 " pdb=" N ASN D 532 " pdb=" CA ASN D 532 " ideal model delta harmonic sigma weight residual 180.00 -152.87 -27.13 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA THR B1160 " pdb=" C THR B1160 " pdb=" N SER B1161 " pdb=" CA SER B1161 " ideal model delta harmonic sigma weight residual -180.00 -156.16 -23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 57.14 35.86 1 1.00e+01 1.00e-02 1.82e+01 ... (remaining 18376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3980 0.055 - 0.110: 616 0.110 - 0.164: 84 0.164 - 0.219: 0 0.219 - 0.274: 4 Chirality restraints: 4684 Sorted by residual: chirality pdb=" CA CYS D 361 " pdb=" N CYS D 361 " pdb=" C CYS D 361 " pdb=" CB CYS D 361 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ALA D 363 " pdb=" N ALA D 363 " pdb=" C ALA D 363 " pdb=" CB ALA D 363 " both_signs ideal model delta sigma weight residual False 2.48 2.22 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA VAL D 362 " pdb=" N VAL D 362 " pdb=" C VAL D 362 " pdb=" CB VAL D 362 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 4681 not shown) Planarity restraints: 5455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO A 295 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 290 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C ASP A 290 " 0.029 2.00e-02 2.50e+03 pdb=" O ASP A 290 " -0.011 2.00e-02 2.50e+03 pdb=" N CYS A 291 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 714 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 715 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 715 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 715 " 0.023 5.00e-02 4.00e+02 ... (remaining 5452 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 312 2.65 - 3.21: 26795 3.21 - 3.78: 43868 3.78 - 4.34: 61785 4.34 - 4.90: 100840 Nonbonded interactions: 233600 Sorted by model distance: nonbonded pdb=" NH2 ARG A 273 " pdb=" O CYS A 291 " model vdw 2.091 2.520 nonbonded pdb=" O VAL B 327 " pdb=" OG1 THR B 531 " model vdw 2.135 2.440 nonbonded pdb=" OG1 THR A 883 " pdb=" OH TYR B 707 " model vdw 2.169 2.440 nonbonded pdb=" OG1 THR D 108 " pdb=" O ASN D 234 " model vdw 2.195 2.440 nonbonded pdb=" OG SER D 746 " pdb=" OE1 GLU D 748 " model vdw 2.205 2.440 ... (remaining 233595 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' and (resid 14 through 255 or resid 257 through 1157)) selection = (chain 'B' and (resid 14 through 291 or (resid 292 and (name N or name CA or nam \ e C or name O )) or resid 293 through 1157)) selection = (chain 'D' and (resid 14 through 255 or resid 257 through 291 or (resid 292 and \ (name N or name CA or name C or name O )) or resid 293 through 1157)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 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: 11.120 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 76.370 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 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 : 0.003 0.233 30924 Z= 0.179 Angle : 0.502 8.844 42053 Z= 0.301 Chirality : 0.041 0.274 4684 Planarity : 0.003 0.055 5455 Dihedral : 7.889 80.060 11087 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.96 % Favored : 95.86 % Rotamer: Outliers : 0.03 % Allowed : 0.15 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -2.30 (0.11), residues: 3791 helix: -3.17 (0.10), residues: 944 sheet: -0.49 (0.17), residues: 665 loop : -1.03 (0.12), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 152 HIS 0.006 0.001 HIS D 242 PHE 0.018 0.001 PHE B 464 TYR 0.016 0.001 TYR A 495 ARG 0.003 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 929 time to evaluate : 3.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8742 (mp) cc_final: 0.8428 (mm) REVERT: A 177 MET cc_start: 0.1855 (ttm) cc_final: -0.0360 (mtm) REVERT: A 280 ASN cc_start: 0.6734 (p0) cc_final: 0.6437 (p0) REVERT: A 408 ARG cc_start: 0.7332 (ptt180) cc_final: 0.6889 (tpt-90) REVERT: A 732 THR cc_start: 0.8983 (m) cc_final: 0.8635 (p) REVERT: A 775 ASP cc_start: 0.8930 (m-30) cc_final: 0.7641 (m-30) REVERT: A 992 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8703 (mm-40) REVERT: A 1001 LEU cc_start: 0.9354 (mt) cc_final: 0.9115 (mt) REVERT: A 1011 GLN cc_start: 0.9076 (mm110) cc_final: 0.8616 (mp10) REVERT: A 1028 LYS cc_start: 0.9149 (mmtp) cc_final: 0.8924 (mmmm) REVERT: A 1029 MET cc_start: 0.9197 (tpp) cc_final: 0.8700 (tpp) REVERT: A 1040 VAL cc_start: 0.7858 (t) cc_final: 0.7612 (m) REVERT: A 1055 SER cc_start: 0.9233 (t) cc_final: 0.8573 (p) REVERT: A 1064 HIS cc_start: 0.7000 (m-70) cc_final: 0.4995 (m-70) REVERT: D 55 PHE cc_start: 0.7893 (m-10) cc_final: 0.7458 (m-10) REVERT: D 133 PHE cc_start: 0.4777 (m-10) cc_final: 0.4025 (m-10) REVERT: D 224 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7576 (pt0) REVERT: D 284 THR cc_start: 0.9324 (m) cc_final: 0.9027 (p) REVERT: D 287 ASP cc_start: 0.7514 (t0) cc_final: 0.7179 (t0) REVERT: D 293 LEU cc_start: 0.8448 (tp) cc_final: 0.8244 (tt) REVERT: D 377 PHE cc_start: 0.5635 (m-10) cc_final: 0.2435 (t80) REVERT: D 598 ILE cc_start: 0.9399 (mp) cc_final: 0.9183 (mp) REVERT: D 721 SER cc_start: 0.8645 (t) cc_final: 0.8324 (p) REVERT: D 730 SER cc_start: 0.9079 (p) cc_final: 0.8542 (t) REVERT: D 761 THR cc_start: 0.8304 (m) cc_final: 0.7999 (m) REVERT: D 770 ILE cc_start: 0.9332 (mt) cc_final: 0.8587 (mm) REVERT: D 780 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7887 (mt-10) REVERT: D 797 PHE cc_start: 0.6085 (m-10) cc_final: 0.5873 (m-80) REVERT: D 915 VAL cc_start: 0.8860 (t) cc_final: 0.8656 (t) REVERT: D 954 GLN cc_start: 0.8536 (tp40) cc_final: 0.8123 (tp40) REVERT: D 1023 ASN cc_start: 0.9248 (m-40) cc_final: 0.9010 (m-40) REVERT: D 1033 VAL cc_start: 0.9237 (t) cc_final: 0.8769 (t) REVERT: D 1040 VAL cc_start: 0.7253 (t) cc_final: 0.6652 (m) REVERT: C 37 GLU cc_start: 0.6519 (tt0) cc_final: 0.6244 (tt0) REVERT: C 62 MET cc_start: 0.7437 (ttp) cc_final: 0.7196 (mtp) REVERT: C 64 ASN cc_start: 0.8070 (m-40) cc_final: 0.7699 (t0) REVERT: C 106 SER cc_start: 0.7435 (m) cc_final: 0.6850 (m) REVERT: C 274 PHE cc_start: 0.8228 (p90) cc_final: 0.7971 (m-80) REVERT: C 383 MET cc_start: 0.2560 (mtp) cc_final: 0.1312 (ppp) REVERT: C 555 PHE cc_start: 0.3751 (t80) cc_final: 0.3294 (t80) REVERT: C 585 LEU cc_start: 0.7484 (tp) cc_final: 0.7089 (pp) REVERT: B 86 PHE cc_start: 0.7449 (t80) cc_final: 0.6686 (t80) REVERT: B 91 TYR cc_start: 0.8158 (t80) cc_final: 0.7935 (t80) REVERT: B 92 PHE cc_start: 0.7456 (m-10) cc_final: 0.6996 (m-80) REVERT: B 106 PHE cc_start: 0.9051 (m-10) cc_final: 0.8344 (m-80) REVERT: B 117 LEU cc_start: 0.8951 (tp) cc_final: 0.8537 (mt) REVERT: B 180 GLU cc_start: 0.6949 (tt0) cc_final: 0.6667 (mm-30) REVERT: B 194 PHE cc_start: 0.6717 (m-10) cc_final: 0.6179 (m-10) REVERT: B 302 THR cc_start: 0.8764 (m) cc_final: 0.8546 (m) REVERT: B 315 THR cc_start: 0.8565 (p) cc_final: 0.8365 (m) REVERT: B 417 ASN cc_start: 0.9106 (m-40) cc_final: 0.8760 (p0) REVERT: B 449 TYR cc_start: 0.8474 (m-10) cc_final: 0.8241 (m-80) REVERT: B 802 PHE cc_start: 0.8844 (m-80) cc_final: 0.8587 (m-80) REVERT: B 819 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8111 (mt-10) REVERT: B 867 ASP cc_start: 0.8660 (m-30) cc_final: 0.8389 (p0) REVERT: B 868 GLU cc_start: 0.8265 (tp30) cc_final: 0.7877 (tp30) REVERT: B 922 LEU cc_start: 0.9073 (tp) cc_final: 0.8187 (tp) REVERT: B 959 LEU cc_start: 0.9498 (mt) cc_final: 0.9256 (mm) REVERT: B 1029 MET cc_start: 0.8939 (tpp) cc_final: 0.8632 (tpp) REVERT: B 1043 CYS cc_start: 0.3797 (m) cc_final: 0.3302 (m) REVERT: B 1104 VAL cc_start: 0.9158 (t) cc_final: 0.8838 (p) outliers start: 1 outliers final: 0 residues processed: 930 average time/residue: 0.4257 time to fit residues: 625.9909 Evaluate side-chains 513 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 9.9990 chunk 288 optimal weight: 2.9990 chunk 159 optimal weight: 0.1980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 297 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 181 optimal weight: 0.2980 chunk 221 optimal weight: 9.9990 chunk 345 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 544 ASN A 563 GLN A 901 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 HIS D 317 ASN D 360 ASN D 563 GLN D 613 GLN D 925 ASN D 949 GLN D 965 GLN C 24 GLN C 58 ASN C 380 GLN C 388 GLN C 401 HIS C 417 HIS C 526 GLN C 552 GLN C 580 ASN B 61 ASN B 81 ASN B 99 ASN B 239 GLN B 370 ASN B 394 ASN B 556 ASN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN B1113 GLN B1142 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30924 Z= 0.229 Angle : 0.630 10.468 42053 Z= 0.330 Chirality : 0.045 0.207 4684 Planarity : 0.004 0.052 5455 Dihedral : 3.998 28.569 4105 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.71 % Favored : 98.26 % Rotamer: Outliers : 2.50 % Allowed : 10.32 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.88 (0.12), residues: 3791 helix: -0.38 (0.15), residues: 950 sheet: -0.18 (0.17), residues: 662 loop : -0.76 (0.12), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 258 HIS 0.007 0.001 HIS A1064 PHE 0.031 0.002 PHE B 157 TYR 0.024 0.002 TYR D1007 ARG 0.009 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 525 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.2107 (ttm) cc_final: 0.0578 (mtm) REVERT: A 776 LYS cc_start: 0.9336 (tppt) cc_final: 0.8886 (tppt) REVERT: A 780 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7808 (mm-30) REVERT: A 992 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8286 (mp10) REVERT: A 1011 GLN cc_start: 0.9180 (mm110) cc_final: 0.8642 (mp10) REVERT: A 1029 MET cc_start: 0.9441 (tpp) cc_final: 0.9191 (tpp) REVERT: A 1068 VAL cc_start: 0.8829 (t) cc_final: 0.8504 (p) REVERT: D 55 PHE cc_start: 0.7534 (m-10) cc_final: 0.6768 (m-10) REVERT: D 284 THR cc_start: 0.9358 (m) cc_final: 0.9073 (p) REVERT: D 377 PHE cc_start: 0.5697 (m-10) cc_final: 0.2240 (t80) REVERT: D 730 SER cc_start: 0.9206 (p) cc_final: 0.8747 (t) REVERT: D 776 LYS cc_start: 0.9377 (ttmm) cc_final: 0.8627 (ttpp) REVERT: D 777 ASN cc_start: 0.9175 (m-40) cc_final: 0.8824 (t0) REVERT: D 779 GLN cc_start: 0.9211 (mt0) cc_final: 0.8944 (tp-100) REVERT: D 797 PHE cc_start: 0.6315 (m-10) cc_final: 0.6034 (m-80) REVERT: D 869 MET cc_start: 0.9232 (mtp) cc_final: 0.8821 (mtm) REVERT: D 948 LEU cc_start: 0.9102 (mt) cc_final: 0.8753 (mp) REVERT: D 955 ASN cc_start: 0.9174 (m-40) cc_final: 0.8731 (m110) REVERT: D 1040 VAL cc_start: 0.7373 (t) cc_final: 0.6822 (t) REVERT: D 1122 VAL cc_start: 0.8770 (p) cc_final: 0.8521 (p) REVERT: C 45 LEU cc_start: 0.7952 (tp) cc_final: 0.7611 (pp) REVERT: C 64 ASN cc_start: 0.8118 (m-40) cc_final: 0.7735 (t0) REVERT: C 152 MET cc_start: -0.5557 (mtt) cc_final: -0.6078 (mmt) REVERT: C 274 PHE cc_start: 0.8374 (p90) cc_final: 0.8023 (m-80) REVERT: C 383 MET cc_start: 0.2623 (mtp) cc_final: 0.1407 (ppp) REVERT: C 585 LEU cc_start: 0.7254 (tp) cc_final: 0.6864 (pp) REVERT: B 86 PHE cc_start: 0.7332 (t80) cc_final: 0.6744 (t80) REVERT: B 117 LEU cc_start: 0.9088 (tp) cc_final: 0.8515 (mp) REVERT: B 180 GLU cc_start: 0.7153 (tt0) cc_final: 0.6861 (mm-30) REVERT: B 194 PHE cc_start: 0.6116 (m-10) cc_final: 0.5652 (m-10) REVERT: B 229 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7708 (mm) REVERT: B 302 THR cc_start: 0.8778 (m) cc_final: 0.8354 (m) REVERT: B 417 ASN cc_start: 0.9072 (m-40) cc_final: 0.8563 (t0) REVERT: B 725 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 770 ILE cc_start: 0.9548 (mm) cc_final: 0.9325 (mm) REVERT: B 774 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8865 (mm110) REVERT: B 867 ASP cc_start: 0.8872 (m-30) cc_final: 0.8650 (p0) REVERT: B 868 GLU cc_start: 0.8644 (tp30) cc_final: 0.8300 (tp30) REVERT: B 918 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8729 (mt-10) REVERT: B 922 LEU cc_start: 0.9026 (tp) cc_final: 0.8772 (tp) REVERT: B 936 ASP cc_start: 0.9083 (OUTLIER) cc_final: 0.8860 (p0) REVERT: B 1040 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8585 (p) REVERT: B 1043 CYS cc_start: 0.4724 (m) cc_final: 0.4319 (m) REVERT: B 1104 VAL cc_start: 0.9338 (t) cc_final: 0.9089 (p) outliers start: 84 outliers final: 55 residues processed: 570 average time/residue: 0.4183 time to fit residues: 382.8998 Evaluate side-chains 471 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 413 time to evaluate : 3.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 821 LEU Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 925 ASN Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1113 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 287 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 345 optimal weight: 10.0000 chunk 373 optimal weight: 7.9990 chunk 307 optimal weight: 7.9990 chunk 342 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 277 optimal weight: 0.0470 overall best weight: 2.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 474 GLN A 762 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 GLN D 606 ASN ** D 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN D1142 GLN C 58 ASN C 103 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1048 HIS ** B1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 30924 Z= 0.289 Angle : 0.662 9.436 42053 Z= 0.348 Chirality : 0.046 0.200 4684 Planarity : 0.005 0.069 5455 Dihedral : 4.339 24.544 4105 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 3.76 % Allowed : 10.85 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.57 (0.13), residues: 3791 helix: 0.26 (0.16), residues: 1013 sheet: -0.04 (0.18), residues: 670 loop : -0.78 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 104 HIS 0.007 0.002 HIS B1159 PHE 0.033 0.002 PHE A 759 TYR 0.024 0.002 TYR A 917 ARG 0.010 0.001 ARG C 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 407 time to evaluate : 3.480 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 55 PHE cc_start: 0.7666 (m-10) cc_final: 0.7180 (m-10) REVERT: A 177 MET cc_start: 0.2680 (ttm) cc_final: 0.0179 (mtp) REVERT: A 747 THR cc_start: 0.9414 (m) cc_final: 0.9069 (p) REVERT: A 761 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8841 (m) REVERT: A 1011 GLN cc_start: 0.9285 (mm110) cc_final: 0.8956 (mm110) REVERT: A 1029 MET cc_start: 0.9542 (tpp) cc_final: 0.9049 (tpp) REVERT: A 1030 SER cc_start: 0.9640 (m) cc_final: 0.9431 (p) REVERT: A 1068 VAL cc_start: 0.9215 (t) cc_final: 0.8924 (p) REVERT: D 55 PHE cc_start: 0.7834 (m-10) cc_final: 0.7247 (m-10) REVERT: D 133 PHE cc_start: 0.6025 (m-10) cc_final: 0.5276 (m-10) REVERT: D 148 ASN cc_start: 0.8526 (m-40) cc_final: 0.8076 (t0) REVERT: D 177 MET cc_start: 0.2869 (ttm) cc_final: 0.2563 (ttm) REVERT: D 730 SER cc_start: 0.9419 (p) cc_final: 0.8862 (t) REVERT: D 775 ASP cc_start: 0.9332 (m-30) cc_final: 0.8933 (t0) REVERT: D 955 ASN cc_start: 0.9230 (m-40) cc_final: 0.8742 (m110) REVERT: D 1002 GLN cc_start: 0.9069 (tt0) cc_final: 0.8579 (tm-30) REVERT: D 1029 MET cc_start: 0.9386 (tpp) cc_final: 0.9144 (tpp) REVERT: C 152 MET cc_start: -0.5412 (mtt) cc_final: -0.5774 (mmt) REVERT: C 383 MET cc_start: 0.2232 (mtp) cc_final: 0.1263 (ppp) REVERT: B 92 PHE cc_start: 0.7989 (m-10) cc_final: 0.7133 (m-10) REVERT: B 117 LEU cc_start: 0.9187 (tp) cc_final: 0.8384 (mp) REVERT: B 118 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9052 (mp) REVERT: B 180 GLU cc_start: 0.7606 (tt0) cc_final: 0.7204 (mm-30) REVERT: B 194 PHE cc_start: 0.6829 (m-10) cc_final: 0.6017 (m-10) REVERT: B 417 ASN cc_start: 0.9189 (m-40) cc_final: 0.8680 (t0) REVERT: B 774 GLN cc_start: 0.9356 (mm-40) cc_final: 0.8904 (mm-40) REVERT: B 867 ASP cc_start: 0.9034 (m-30) cc_final: 0.8644 (p0) REVERT: B 868 GLU cc_start: 0.8667 (tp30) cc_final: 0.8373 (tp30) REVERT: B 900 MET cc_start: 0.8774 (mmt) cc_final: 0.8516 (mmt) REVERT: B 904 TYR cc_start: 0.8771 (t80) cc_final: 0.8489 (t80) REVERT: B 918 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8759 (mt-10) REVERT: B 922 LEU cc_start: 0.8913 (tp) cc_final: 0.8692 (tp) REVERT: B 936 ASP cc_start: 0.9105 (OUTLIER) cc_final: 0.8858 (p0) REVERT: B 954 GLN cc_start: 0.9156 (mt0) cc_final: 0.8883 (mt0) REVERT: B 1010 GLN cc_start: 0.9281 (mm-40) cc_final: 0.9013 (tm-30) REVERT: B 1023 ASN cc_start: 0.9472 (t0) cc_final: 0.9108 (t0) REVERT: B 1040 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8863 (p) outliers start: 126 outliers final: 73 residues processed: 484 average time/residue: 0.3756 time to fit residues: 299.9167 Evaluate side-chains 417 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 340 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 0.0040 chunk 259 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 38 optimal weight: 30.0000 chunk 164 optimal weight: 0.0570 chunk 232 optimal weight: 9.9990 chunk 346 optimal weight: 3.9990 chunk 367 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 328 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 overall best weight: 0.5914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 751 ASN A 762 GLN A 787 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS D 613 GLN D1005 GLN C 345 HIS C 508 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1083 HIS B1113 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 30924 Z= 0.154 Angle : 0.561 8.653 42053 Z= 0.287 Chirality : 0.044 0.198 4684 Planarity : 0.004 0.062 5455 Dihedral : 4.072 23.041 4105 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.08 % Favored : 97.89 % Rotamer: Outliers : 2.83 % Allowed : 12.91 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.36 (0.13), residues: 3791 helix: 0.61 (0.16), residues: 997 sheet: 0.09 (0.19), residues: 646 loop : -0.73 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 104 HIS 0.005 0.001 HIS C 345 PHE 0.026 0.001 PHE D 782 TYR 0.028 0.001 TYR A 145 ARG 0.004 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 410 time to evaluate : 3.197 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: A 55 PHE cc_start: 0.7457 (m-80) cc_final: 0.7142 (m-10) REVERT: A 177 MET cc_start: 0.2035 (ttm) cc_final: -0.0230 (mtp) REVERT: A 737 ASP cc_start: 0.7886 (p0) cc_final: 0.7205 (p0) REVERT: A 776 LYS cc_start: 0.9459 (tppt) cc_final: 0.9115 (tppt) REVERT: A 1011 GLN cc_start: 0.9202 (mm110) cc_final: 0.8791 (mp10) REVERT: A 1068 VAL cc_start: 0.9184 (t) cc_final: 0.8909 (p) REVERT: A 1138 TYR cc_start: 0.8975 (m-80) cc_final: 0.8692 (m-80) REVERT: D 55 PHE cc_start: 0.7960 (m-10) cc_final: 0.7461 (m-10) REVERT: D 133 PHE cc_start: 0.5851 (m-10) cc_final: 0.5121 (m-10) REVERT: D 148 ASN cc_start: 0.8481 (m-40) cc_final: 0.8091 (t0) REVERT: D 284 THR cc_start: 0.9406 (m) cc_final: 0.9145 (p) REVERT: D 730 SER cc_start: 0.9236 (p) cc_final: 0.9003 (t) REVERT: D 775 ASP cc_start: 0.9204 (m-30) cc_final: 0.8815 (t70) REVERT: D 955 ASN cc_start: 0.9228 (m-40) cc_final: 0.8721 (m110) REVERT: D 962 LEU cc_start: 0.9391 (tp) cc_final: 0.9160 (tp) REVERT: D 970 PHE cc_start: 0.7894 (m-10) cc_final: 0.7678 (m-10) REVERT: D 1002 GLN cc_start: 0.9046 (tt0) cc_final: 0.8808 (tt0) REVERT: D 1011 GLN cc_start: 0.9215 (mm110) cc_final: 0.8610 (mm-40) REVERT: D 1073 LYS cc_start: 0.8622 (ptpp) cc_final: 0.8188 (ptpp) REVERT: C 82 MET cc_start: 0.6681 (mmm) cc_final: 0.6440 (mmp) REVERT: C 152 MET cc_start: -0.5350 (mtt) cc_final: -0.5770 (mmt) REVERT: C 383 MET cc_start: 0.1710 (mtp) cc_final: 0.0737 (tmm) REVERT: C 474 MET cc_start: -0.4244 (mmt) cc_final: -0.4484 (mmt) REVERT: B 117 LEU cc_start: 0.9133 (tp) cc_final: 0.8316 (mp) REVERT: B 118 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9030 (mp) REVERT: B 180 GLU cc_start: 0.7197 (tt0) cc_final: 0.6852 (mm-30) REVERT: B 191 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8956 (mm-30) REVERT: B 417 ASN cc_start: 0.9149 (m-40) cc_final: 0.8639 (t0) REVERT: B 725 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7898 (mt-10) REVERT: B 774 GLN cc_start: 0.9255 (mm-40) cc_final: 0.8854 (mm110) REVERT: B 867 ASP cc_start: 0.9011 (m-30) cc_final: 0.8607 (p0) REVERT: B 868 GLU cc_start: 0.8621 (tp30) cc_final: 0.8303 (tp30) REVERT: B 900 MET cc_start: 0.8673 (mmt) cc_final: 0.8449 (mmt) REVERT: B 922 LEU cc_start: 0.8932 (tp) cc_final: 0.8634 (tp) REVERT: B 1040 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.9032 (p) outliers start: 95 outliers final: 63 residues processed: 467 average time/residue: 0.3849 time to fit residues: 294.1395 Evaluate side-chains 422 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 357 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 978 ASN Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1096 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 273 optimal weight: 20.0000 chunk 151 optimal weight: 0.9980 chunk 313 optimal weight: 9.9990 chunk 253 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 187 optimal weight: 0.9980 chunk 329 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 394 ASN A 474 GLN A 544 ASN A 658 ASN A 762 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 ASN D 188 ASN ** D 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 901 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 30924 Z= 0.285 Angle : 0.638 9.340 42053 Z= 0.336 Chirality : 0.045 0.303 4684 Planarity : 0.004 0.061 5455 Dihedral : 4.399 24.361 4105 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 3.55 % Allowed : 12.85 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.51 (0.13), residues: 3791 helix: 0.46 (0.16), residues: 1018 sheet: -0.00 (0.19), residues: 676 loop : -0.83 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 886 HIS 0.041 0.002 HIS C 345 PHE 0.021 0.002 PHE A 759 TYR 0.021 0.002 TYR A 145 ARG 0.006 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 341 time to evaluate : 3.709 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: A 177 MET cc_start: 0.3097 (ttm) cc_final: 0.2585 (ttm) REVERT: A 751 ASN cc_start: 0.9485 (OUTLIER) cc_final: 0.9265 (p0) REVERT: A 904 TYR cc_start: 0.7901 (m-80) cc_final: 0.7680 (m-80) REVERT: A 1011 GLN cc_start: 0.9272 (mm110) cc_final: 0.8866 (mm110) REVERT: A 1068 VAL cc_start: 0.9333 (t) cc_final: 0.9055 (p) REVERT: A 1138 TYR cc_start: 0.9087 (m-80) cc_final: 0.8784 (m-80) REVERT: D 55 PHE cc_start: 0.8131 (m-10) cc_final: 0.7697 (m-10) REVERT: D 133 PHE cc_start: 0.6626 (m-10) cc_final: 0.5707 (m-10) REVERT: D 148 ASN cc_start: 0.8600 (m-40) cc_final: 0.8385 (m-40) REVERT: D 730 SER cc_start: 0.9389 (p) cc_final: 0.9156 (t) REVERT: D 1011 GLN cc_start: 0.9211 (mm110) cc_final: 0.8594 (mm-40) REVERT: C 152 MET cc_start: -0.5290 (mtt) cc_final: -0.5833 (mmt) REVERT: C 323 MET cc_start: -0.0025 (mmt) cc_final: -0.1853 (mmm) REVERT: C 383 MET cc_start: 0.1582 (mtp) cc_final: 0.0993 (ttp) REVERT: B 117 LEU cc_start: 0.9152 (tp) cc_final: 0.8501 (mp) REVERT: B 180 GLU cc_start: 0.7583 (tt0) cc_final: 0.7134 (tp30) REVERT: B 417 ASN cc_start: 0.9183 (m-40) cc_final: 0.8629 (t0) REVERT: B 449 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8178 (m-10) REVERT: B 725 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7714 (mt-10) REVERT: B 774 GLN cc_start: 0.9208 (mm-40) cc_final: 0.8850 (mm110) REVERT: B 864 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8720 (tp) REVERT: B 867 ASP cc_start: 0.9093 (m-30) cc_final: 0.8661 (p0) REVERT: B 868 GLU cc_start: 0.8667 (tp30) cc_final: 0.8372 (tp30) REVERT: B 900 MET cc_start: 0.9029 (mmt) cc_final: 0.8797 (mmt) REVERT: B 918 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8894 (mt-10) REVERT: B 1040 VAL cc_start: 0.9422 (t) cc_final: 0.9179 (p) outliers start: 119 outliers final: 80 residues processed: 423 average time/residue: 0.3832 time to fit residues: 268.2834 Evaluate side-chains 396 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 313 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 607 GLN Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 10.0000 chunk 330 optimal weight: 0.0980 chunk 72 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 90 optimal weight: 0.0470 chunk 367 optimal weight: 0.9990 chunk 305 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 overall best weight: 1.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 751 ASN A 762 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN D 957 GLN D1005 GLN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.6261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30924 Z= 0.171 Angle : 0.553 7.185 42053 Z= 0.286 Chirality : 0.043 0.186 4684 Planarity : 0.004 0.058 5455 Dihedral : 4.175 22.343 4105 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 2.80 % Allowed : 14.07 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.36 (0.13), residues: 3791 helix: 0.69 (0.16), residues: 1012 sheet: -0.01 (0.19), residues: 668 loop : -0.76 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 104 HIS 0.007 0.001 HIS B1159 PHE 0.024 0.001 PHE A 759 TYR 0.021 0.001 TYR A 145 ARG 0.005 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 369 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.2719 (ttm) cc_final: 0.2276 (ttm) REVERT: A 902 MET cc_start: 0.9279 (mmm) cc_final: 0.9049 (mmp) REVERT: A 904 TYR cc_start: 0.7847 (m-80) cc_final: 0.7514 (m-80) REVERT: A 1011 GLN cc_start: 0.9240 (mm110) cc_final: 0.9024 (mm110) REVERT: A 1029 MET cc_start: 0.9397 (tpp) cc_final: 0.8889 (tpp) REVERT: A 1068 VAL cc_start: 0.9296 (t) cc_final: 0.9022 (p) REVERT: A 1138 TYR cc_start: 0.9117 (m-80) cc_final: 0.8827 (m-80) REVERT: D 55 PHE cc_start: 0.8102 (m-10) cc_final: 0.7289 (m-80) REVERT: D 133 PHE cc_start: 0.6466 (m-10) cc_final: 0.5560 (m-10) REVERT: D 177 MET cc_start: 0.2507 (tpp) cc_final: 0.2245 (tpp) REVERT: D 775 ASP cc_start: 0.9029 (m-30) cc_final: 0.8725 (t0) REVERT: D 970 PHE cc_start: 0.8128 (m-10) cc_final: 0.7928 (m-10) REVERT: D 1002 GLN cc_start: 0.9054 (tt0) cc_final: 0.8586 (tm-30) REVERT: D 1011 GLN cc_start: 0.9250 (mm110) cc_final: 0.8585 (mm-40) REVERT: C 152 MET cc_start: -0.5222 (mtt) cc_final: -0.5737 (mmt) REVERT: C 323 MET cc_start: 0.0039 (mmt) cc_final: -0.1529 (mmm) REVERT: C 383 MET cc_start: 0.1529 (mtp) cc_final: 0.1026 (ttp) REVERT: B 117 LEU cc_start: 0.9177 (tp) cc_final: 0.8450 (mp) REVERT: B 180 GLU cc_start: 0.7162 (tt0) cc_final: 0.6793 (tp30) REVERT: B 417 ASN cc_start: 0.9159 (m-40) cc_final: 0.8600 (t0) REVERT: B 449 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.8179 (m-10) REVERT: B 661 GLU cc_start: 0.7781 (tp30) cc_final: 0.7579 (tp30) REVERT: B 725 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7729 (mt-10) REVERT: B 774 GLN cc_start: 0.9253 (mm-40) cc_final: 0.8944 (mm110) REVERT: B 867 ASP cc_start: 0.9079 (m-30) cc_final: 0.8600 (p0) REVERT: B 868 GLU cc_start: 0.8649 (tp30) cc_final: 0.8352 (tp30) REVERT: B 900 MET cc_start: 0.8884 (mmt) cc_final: 0.8626 (mmt) REVERT: B 1092 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7883 (tm-30) outliers start: 94 outliers final: 72 residues processed: 436 average time/residue: 0.3688 time to fit residues: 269.6466 Evaluate side-chains 409 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 336 time to evaluate : 3.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 978 ASN Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1017 GLU Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1137 VAL Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 209 optimal weight: 0.0770 chunk 268 optimal weight: 5.9990 chunk 208 optimal weight: 0.9980 chunk 309 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 366 optimal weight: 6.9990 chunk 229 optimal weight: 20.0000 chunk 223 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 overall best weight: 2.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 949 GLN D 954 GLN C 508 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.6755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30924 Z= 0.216 Angle : 0.587 9.605 42053 Z= 0.306 Chirality : 0.044 0.183 4684 Planarity : 0.004 0.058 5455 Dihedral : 4.278 25.530 4105 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.01 % Allowed : 14.52 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.43 (0.13), residues: 3791 helix: 0.70 (0.16), residues: 1021 sheet: -0.13 (0.19), residues: 681 loop : -0.81 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 104 HIS 0.008 0.001 HIS B1159 PHE 0.028 0.002 PHE A 759 TYR 0.022 0.001 TYR B 904 ARG 0.006 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 344 time to evaluate : 3.348 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 177 MET cc_start: 0.2849 (ttm) cc_final: 0.2416 (ttm) REVERT: A 1138 TYR cc_start: 0.9094 (m-80) cc_final: 0.8796 (m-80) REVERT: D 55 PHE cc_start: 0.8218 (m-10) cc_final: 0.7410 (m-80) REVERT: D 104 TRP cc_start: 0.8381 (m-10) cc_final: 0.7735 (m-90) REVERT: D 105 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7468 (tp) REVERT: D 133 PHE cc_start: 0.6861 (m-10) cc_final: 0.5802 (m-10) REVERT: D 177 MET cc_start: 0.2526 (tpp) cc_final: 0.2185 (tpp) REVERT: D 730 SER cc_start: 0.9303 (p) cc_final: 0.9103 (t) REVERT: D 775 ASP cc_start: 0.9072 (m-30) cc_final: 0.8740 (t0) REVERT: D 1002 GLN cc_start: 0.9024 (tt0) cc_final: 0.8620 (tm-30) REVERT: D 1011 GLN cc_start: 0.9166 (mm110) cc_final: 0.8893 (tp40) REVERT: D 1050 MET cc_start: 0.8442 (ptp) cc_final: 0.7941 (ptp) REVERT: C 152 MET cc_start: -0.5132 (mtt) cc_final: -0.5644 (mmt) REVERT: C 323 MET cc_start: -0.0080 (mmt) cc_final: -0.1875 (mmm) REVERT: C 383 MET cc_start: 0.1553 (mtp) cc_final: 0.0812 (ttp) REVERT: B 117 LEU cc_start: 0.9208 (tp) cc_final: 0.8498 (mp) REVERT: B 180 GLU cc_start: 0.7333 (tt0) cc_final: 0.6928 (tp30) REVERT: B 417 ASN cc_start: 0.9120 (m-40) cc_final: 0.8544 (t0) REVERT: B 449 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.8292 (m-10) REVERT: B 557 LYS cc_start: 0.7050 (mmtt) cc_final: 0.6756 (mmtm) REVERT: B 725 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7794 (mt-10) REVERT: B 774 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8906 (mm110) REVERT: B 867 ASP cc_start: 0.9111 (m-30) cc_final: 0.8587 (p0) REVERT: B 868 GLU cc_start: 0.8684 (tp30) cc_final: 0.8393 (tp30) REVERT: B 900 MET cc_start: 0.8889 (mmt) cc_final: 0.8623 (mmt) REVERT: B 904 TYR cc_start: 0.8707 (t80) cc_final: 0.8337 (t80) REVERT: B 1041 ASP cc_start: 0.7210 (m-30) cc_final: 0.6354 (m-30) REVERT: B 1045 LYS cc_start: 0.8884 (tppt) cc_final: 0.8672 (tppt) outliers start: 101 outliers final: 84 residues processed: 413 average time/residue: 0.3665 time to fit residues: 252.1084 Evaluate side-chains 395 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 309 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 819 GLU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain D residue 1137 VAL Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 232 optimal weight: 20.0000 chunk 249 optimal weight: 7.9990 chunk 181 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 287 optimal weight: 0.0470 overall best weight: 1.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 474 GLN A 493 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 755 GLN D 872 GLN D 949 GLN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.7094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30924 Z= 0.197 Angle : 0.578 10.478 42053 Z= 0.298 Chirality : 0.044 0.196 4684 Planarity : 0.004 0.062 5455 Dihedral : 4.279 24.262 4105 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.68 % Allowed : 15.35 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.47 (0.13), residues: 3791 helix: 0.70 (0.16), residues: 1029 sheet: -0.19 (0.19), residues: 697 loop : -0.85 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 104 HIS 0.008 0.001 HIS B1159 PHE 0.020 0.001 PHE A 759 TYR 0.029 0.001 TYR B1138 ARG 0.005 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 333 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7338 (pm20) REVERT: A 177 MET cc_start: 0.2667 (ttm) cc_final: 0.2257 (ttm) REVERT: A 902 MET cc_start: 0.9356 (mmp) cc_final: 0.8969 (tpp) REVERT: A 1138 TYR cc_start: 0.9113 (m-80) cc_final: 0.8810 (m-80) REVERT: D 55 PHE cc_start: 0.8258 (m-10) cc_final: 0.7476 (m-80) REVERT: D 104 TRP cc_start: 0.8353 (m-10) cc_final: 0.7839 (m-90) REVERT: D 133 PHE cc_start: 0.6941 (m-10) cc_final: 0.6036 (m-10) REVERT: D 148 ASN cc_start: 0.8515 (m-40) cc_final: 0.7619 (t0) REVERT: D 177 MET cc_start: 0.2629 (tpp) cc_final: 0.2215 (tpp) REVERT: D 775 ASP cc_start: 0.9059 (m-30) cc_final: 0.8713 (t0) REVERT: D 1011 GLN cc_start: 0.9186 (mm110) cc_final: 0.8920 (tp40) REVERT: D 1014 ARG cc_start: 0.8847 (tpp-160) cc_final: 0.8245 (tpp-160) REVERT: D 1073 LYS cc_start: 0.8513 (ptpp) cc_final: 0.8312 (ptpp) REVERT: C 152 MET cc_start: -0.4918 (mtt) cc_final: -0.5450 (mmt) REVERT: C 323 MET cc_start: -0.0354 (mmt) cc_final: -0.2005 (mmm) REVERT: C 383 MET cc_start: 0.1597 (mtp) cc_final: 0.0854 (ttp) REVERT: C 474 MET cc_start: -0.4189 (mmt) cc_final: -0.4583 (mmt) REVERT: B 117 LEU cc_start: 0.9206 (tp) cc_final: 0.8498 (mp) REVERT: B 180 GLU cc_start: 0.7319 (tt0) cc_final: 0.6933 (tp30) REVERT: B 191 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8871 (mm-30) REVERT: B 417 ASN cc_start: 0.9107 (m-40) cc_final: 0.8529 (t0) REVERT: B 449 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.8351 (m-10) REVERT: B 557 LYS cc_start: 0.6940 (mmtt) cc_final: 0.6688 (mmtm) REVERT: B 725 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7811 (mt-10) REVERT: B 774 GLN cc_start: 0.9232 (mm-40) cc_final: 0.8916 (mm110) REVERT: B 775 ASP cc_start: 0.8559 (m-30) cc_final: 0.8319 (t0) REVERT: B 867 ASP cc_start: 0.9121 (m-30) cc_final: 0.8539 (p0) REVERT: B 868 GLU cc_start: 0.8658 (tp30) cc_final: 0.8325 (tp30) REVERT: B 900 MET cc_start: 0.8879 (mmt) cc_final: 0.8622 (mmt) REVERT: B 1092 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7951 (tm-30) outliers start: 90 outliers final: 77 residues processed: 398 average time/residue: 0.3877 time to fit residues: 253.8161 Evaluate side-chains 393 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 315 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 819 GLU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain D residue 1137 VAL Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 10.0000 chunk 350 optimal weight: 0.6980 chunk 320 optimal weight: 10.0000 chunk 341 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 308 optimal weight: 1.9990 chunk 322 optimal weight: 0.9980 chunk 340 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A1011 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 HIS ** D 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 949 GLN D1002 GLN C 505 HIS ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 ASN B 607 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.7631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30924 Z= 0.265 Angle : 0.638 10.251 42053 Z= 0.332 Chirality : 0.045 0.202 4684 Planarity : 0.004 0.060 5455 Dihedral : 4.532 26.691 4105 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.07 % Allowed : 15.35 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.63 (0.13), residues: 3791 helix: 0.53 (0.16), residues: 1038 sheet: -0.30 (0.19), residues: 685 loop : -0.93 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 886 HIS 0.010 0.001 HIS B1159 PHE 0.022 0.002 PHE A 759 TYR 0.031 0.002 TYR B 904 ARG 0.012 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 304 time to evaluate : 3.227 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: A 173 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7314 (pm20) REVERT: A 177 MET cc_start: 0.3141 (ttm) cc_final: 0.2626 (ttm) REVERT: A 275 PHE cc_start: 0.7987 (m-10) cc_final: 0.7458 (m-80) REVERT: D 55 PHE cc_start: 0.8328 (m-10) cc_final: 0.7543 (m-80) REVERT: D 104 TRP cc_start: 0.8467 (m-10) cc_final: 0.7902 (m-90) REVERT: D 133 PHE cc_start: 0.7318 (m-10) cc_final: 0.6386 (m-10) REVERT: D 177 MET cc_start: 0.2608 (tpp) cc_final: 0.2224 (tpp) REVERT: D 775 ASP cc_start: 0.9075 (m-30) cc_final: 0.8712 (t0) REVERT: D 1011 GLN cc_start: 0.9187 (mm110) cc_final: 0.8957 (tp40) REVERT: C 152 MET cc_start: -0.4822 (mtt) cc_final: -0.5346 (mmt) REVERT: C 323 MET cc_start: -0.0093 (mmt) cc_final: -0.1756 (mmm) REVERT: C 383 MET cc_start: 0.1259 (mtp) cc_final: 0.0678 (ttp) REVERT: C 474 MET cc_start: -0.4195 (mmt) cc_final: -0.4676 (mmt) REVERT: B 117 LEU cc_start: 0.9201 (tp) cc_final: 0.8516 (mp) REVERT: B 153 MET cc_start: -0.0897 (ptt) cc_final: -0.1180 (ptt) REVERT: B 173 GLN cc_start: 0.7785 (pt0) cc_final: 0.7544 (pp30) REVERT: B 180 GLU cc_start: 0.7480 (tt0) cc_final: 0.7072 (tp30) REVERT: B 417 ASN cc_start: 0.9043 (m-40) cc_final: 0.8500 (t0) REVERT: B 557 LYS cc_start: 0.7262 (mmtt) cc_final: 0.6900 (mmtm) REVERT: B 725 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7763 (mt-10) REVERT: B 775 ASP cc_start: 0.8607 (m-30) cc_final: 0.8308 (t0) REVERT: B 784 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7927 (mm-40) REVERT: B 867 ASP cc_start: 0.9234 (m-30) cc_final: 0.8586 (p0) REVERT: B 868 GLU cc_start: 0.8697 (tp30) cc_final: 0.8421 (tp30) REVERT: B 900 MET cc_start: 0.8940 (mmt) cc_final: 0.8661 (mmt) REVERT: B 1045 LYS cc_start: 0.9137 (tppt) cc_final: 0.8873 (tppt) outliers start: 103 outliers final: 88 residues processed: 375 average time/residue: 0.3779 time to fit residues: 235.8458 Evaluate side-chains 376 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 288 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 819 GLU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain D residue 1137 VAL Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 580 ASN Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 20.0000 chunk 360 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 250 optimal weight: 20.0000 chunk 378 optimal weight: 0.5980 chunk 348 optimal weight: 6.9990 chunk 301 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 232 optimal weight: 20.0000 chunk 184 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A1011 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 HIS D 196 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 949 GLN D1101 HIS ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 GLN C 580 ASN B 774 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.7975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30924 Z= 0.276 Angle : 0.655 14.809 42053 Z= 0.339 Chirality : 0.045 0.190 4684 Planarity : 0.004 0.063 5455 Dihedral : 4.658 23.659 4105 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.95 % Allowed : 15.83 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.78 (0.13), residues: 3791 helix: 0.44 (0.16), residues: 1030 sheet: -0.43 (0.19), residues: 692 loop : -1.03 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 886 HIS 0.010 0.001 HIS B1159 PHE 0.026 0.002 PHE A 464 TYR 0.024 0.002 TYR A 741 ARG 0.007 0.001 ARG B1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7582 Ramachandran restraints generated. 3791 Oldfield, 0 Emsley, 3791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 297 time to evaluate : 3.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7372 (pm20) REVERT: A 177 MET cc_start: 0.3377 (ttm) cc_final: 0.2853 (ttm) REVERT: A 275 PHE cc_start: 0.8091 (m-10) cc_final: 0.7641 (m-80) REVERT: A 902 MET cc_start: 0.9343 (mmp) cc_final: 0.8885 (tpp) REVERT: A 1011 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8744 (mp10) REVERT: A 1041 ASP cc_start: 0.8807 (t70) cc_final: 0.8387 (t70) REVERT: D 55 PHE cc_start: 0.8379 (m-10) cc_final: 0.7613 (m-80) REVERT: D 104 TRP cc_start: 0.8483 (m-10) cc_final: 0.7890 (m-90) REVERT: D 133 PHE cc_start: 0.7423 (m-10) cc_final: 0.6510 (m-10) REVERT: D 177 MET cc_start: 0.2797 (tpp) cc_final: 0.2348 (tpp) REVERT: D 775 ASP cc_start: 0.9053 (m-30) cc_final: 0.8728 (t0) REVERT: D 995 ARG cc_start: 0.9331 (mtt180) cc_final: 0.8803 (ttp-110) REVERT: D 1011 GLN cc_start: 0.9228 (mm110) cc_final: 0.9008 (tp40) REVERT: C 152 MET cc_start: -0.4729 (mtt) cc_final: -0.5304 (mmt) REVERT: C 323 MET cc_start: -0.0081 (mmt) cc_final: -0.1683 (mmm) REVERT: C 383 MET cc_start: 0.1488 (mtp) cc_final: 0.0638 (ttp) REVERT: C 474 MET cc_start: -0.3953 (mmt) cc_final: -0.4406 (mmm) REVERT: B 117 LEU cc_start: 0.9249 (tp) cc_final: 0.8556 (mp) REVERT: B 153 MET cc_start: -0.0743 (ptt) cc_final: -0.1018 (ptt) REVERT: B 180 GLU cc_start: 0.7505 (tt0) cc_final: 0.7092 (tp30) REVERT: B 417 ASN cc_start: 0.9047 (m-40) cc_final: 0.8503 (t0) REVERT: B 557 LYS cc_start: 0.7306 (mmtt) cc_final: 0.6763 (mmtm) REVERT: B 710 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8504 (p0) REVERT: B 725 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7792 (mt-10) REVERT: B 784 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7890 (mm110) REVERT: B 867 ASP cc_start: 0.9264 (m-30) cc_final: 0.8675 (p0) REVERT: B 868 GLU cc_start: 0.8710 (tp30) cc_final: 0.8454 (tp30) REVERT: B 900 MET cc_start: 0.8969 (mmt) cc_final: 0.8665 (mmt) REVERT: B 1041 ASP cc_start: 0.7827 (m-30) cc_final: 0.7111 (m-30) REVERT: B 1138 TYR cc_start: 0.7867 (t80) cc_final: 0.7623 (t80) outliers start: 99 outliers final: 86 residues processed: 370 average time/residue: 0.3950 time to fit residues: 242.5421 Evaluate side-chains 370 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 283 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 819 GLU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1030 SER Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain D residue 1137 VAL Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 580 ASN Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 0.8980 chunk 321 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 277 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 301 optimal weight: 4.9990 chunk 126 optimal weight: 0.0010 chunk 310 optimal weight: 0.0000 chunk 38 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.102403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.086195 restraints weight = 240562.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.087339 restraints weight = 133857.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.088092 restraints weight = 83336.413| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.8002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.282 30924 Z= 0.358 Angle : 0.841 59.113 42053 Z= 0.472 Chirality : 0.047 0.965 4684 Planarity : 0.004 0.092 5455 Dihedral : 4.649 23.807 4105 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.74 % Allowed : 16.19 % Favored : 81.07 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.55 % 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: -0.79 (0.13), residues: 3791 helix: 0.43 (0.16), residues: 1030 sheet: -0.44 (0.19), residues: 692 loop : -1.03 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 886 HIS 0.009 0.001 HIS B1159 PHE 0.049 0.002 PHE D 543 TYR 0.024 0.002 TYR A 741 ARG 0.006 0.001 ARG B1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6472.84 seconds wall clock time: 118 minutes 7.11 seconds (7087.11 seconds total)