Starting phenix.real_space_refine (version: dev) on Mon Feb 27 19:16:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd9_32435/02_2023/7wd9_32435.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd9_32435/02_2023/7wd9_32435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd9_32435/02_2023/7wd9_32435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd9_32435/02_2023/7wd9_32435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd9_32435/02_2023/7wd9_32435.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd9_32435/02_2023/7wd9_32435.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.125 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 69720 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 16708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 16708 Classifications: {'peptide': 1079} Link IDs: {'CIS': 2, 'PTRANS': 52, 'TRANS': 1024} Chain breaks: 8 Chain: "C" Number of atoms: 16708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 16708 Classifications: {'peptide': 1079} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1025} Chain breaks: 8 Chain: "B" Number of atoms: 16708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 16708 Classifications: {'peptide': 1079} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1025} Chain breaks: 8 Chain: "E" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3281 Classifications: {'peptide': 217} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "F" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Chain: "G" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3281 Classifications: {'peptide': 217} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "H" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Chain: "I" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3281 Classifications: {'peptide': 217} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "J" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 24.84, per 1000 atoms: 0.36 Number of scatterers: 69720 At special positions: 0 Unit cell: (219.693, 206.577, 208.763, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 159 16.00 O 6792 8.00 N 5898 7.00 C 22467 6.00 H 34404 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 202 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 138 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 138 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 147 " - pdb=" SG CYS I 202 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 138 " - pdb=" SG CYS J 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 41.09 Conformation dependent library (CDL) restraints added in 4.3 seconds 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8496 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 83 sheets defined 18.7% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.846A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.664A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.855A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 780 removed outlier: 3.752A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 4.212A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.629A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.543A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (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: 3.847A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.612A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.555A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 4.146A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.013A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.988A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.553A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.843A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 780 removed outlier: 3.729A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 4.104A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.210A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.646A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 5.959A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.906A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.526A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.550A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.052A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.925A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.945A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.908A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.886A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 4.120A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 removed outlier: 3.521A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.621A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.546A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.555A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.017A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.634A 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: 3.762A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.540A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 3.964A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.661A pdb=" N SER E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.363A pdb=" N SER E 197 " --> pdb=" O SER E 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.706A pdb=" N ALA F 87 " --> pdb=" O GLU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 131 Processing helix chain 'F' and resid 187 through 192 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.556A pdb=" N PHE G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.651A pdb=" N SER G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 198 removed outlier: 4.524A pdb=" N SER G 197 " --> pdb=" O SER G 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 125 through 131 removed outlier: 3.511A pdb=" N SER H 131 " --> pdb=" O GLU H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 192 Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.643A pdb=" N SER I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 198 removed outlier: 4.359A pdb=" N SER I 197 " --> pdb=" O SER I 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 125 through 131 removed outlier: 3.702A pdb=" N SER J 131 " --> pdb=" O GLU J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.252A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.122A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.547A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.544A pdb=" N GLY A 142 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.661A 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 319 removed outlier: 3.621A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.525A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.852A pdb=" N LYS A 424 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU A 465 " --> pdb=" O LYS A 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 removed outlier: 4.052A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.596A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.685A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.529A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.092A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.151A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.154A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.854A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.433A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.982A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.503A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 325 through 327 removed outlier: 6.770A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.668A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 423 through 424 removed outlier: 3.613A pdb=" N LYS C 424 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU C 465 " --> pdb=" O LYS C 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.508A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 702 through 704 removed outlier: 3.737A pdb=" N LYS B 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AD3, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.572A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.416A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.238A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.104A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.677A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.721A pdb=" N GLY B 142 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.592A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.766A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 376 through 379 removed outlier: 6.133A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.484A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AE8, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.632A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.440A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AF3, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AF4, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.901A pdb=" N MET E 34 " --> pdb=" O MET E 50 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N MET E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG E 40 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.673A pdb=" N CYS E 96 " --> pdb=" O TRP E 110 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TRP E 110 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ARG E 98 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 108 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.559A pdb=" N LYS E 150 " --> pdb=" O SER E 127 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR E 182 " --> pdb=" O GLY E 151 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.559A pdb=" N LYS E 150 " --> pdb=" O SER E 127 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR E 182 " --> pdb=" O GLY E 151 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AF9, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AG1, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.835A pdb=" N TRP F 39 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 10 through 14 removed outlier: 3.814A pdb=" N HIS F 94 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA F 101 " --> pdb=" O HIS F 94 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 30 through 31 Processing sheet with id=AG4, first strand: chain 'F' and resid 118 through 122 removed outlier: 6.084A pdb=" N TYR F 177 " --> pdb=" O ASN F 142 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 157 through 158 Processing sheet with id=AG6, first strand: chain 'G' and resid 3 through 5 Processing sheet with id=AG7, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.657A pdb=" N ASN G 35 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N MET G 34 " --> pdb=" O MET G 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N MET G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG G 40 " --> pdb=" O GLY G 44 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.677A pdb=" N CYS G 96 " --> pdb=" O TRP G 110 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TRP G 110 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG G 98 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA G 108 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 127 through 131 removed outlier: 3.540A pdb=" N LYS G 150 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR G 182 " --> pdb=" O GLY G 151 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 127 through 131 removed outlier: 3.540A pdb=" N LYS G 150 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR G 182 " --> pdb=" O GLY G 151 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 158 through 161 Processing sheet with id=AH3, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AH4, first strand: chain 'H' and resid 10 through 14 removed outlier: 6.793A pdb=" N TRP H 39 " --> pdb=" O LEU H 51 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 10 through 14 removed outlier: 3.653A pdb=" N HIS H 94 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA H 101 " --> pdb=" O HIS H 94 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 30 through 31 Processing sheet with id=AH7, first strand: chain 'H' and resid 118 through 122 removed outlier: 6.124A pdb=" N TYR H 177 " --> pdb=" O ASN H 142 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 157 through 159 removed outlier: 4.114A pdb=" N TRP H 152 " --> pdb=" O ARG H 159 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.608A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.892A pdb=" N ALA I 97 " --> pdb=" O ASN I 35 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN I 35 " --> pdb=" O ALA I 97 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N MET I 34 " --> pdb=" O MET I 50 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N MET I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 9 through 12 removed outlier: 7.257A pdb=" N CYS I 96 " --> pdb=" O TRP I 110 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP I 110 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ARG I 98 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA I 108 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'I' and resid 127 through 131 removed outlier: 3.629A pdb=" N LYS I 150 " --> pdb=" O SER I 127 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR I 182 " --> pdb=" O GLY I 151 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'I' and resid 127 through 131 removed outlier: 3.629A pdb=" N LYS I 150 " --> pdb=" O SER I 127 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR I 182 " --> pdb=" O GLY I 151 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'I' and resid 158 through 161 Processing sheet with id=AI6, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AI7, first strand: chain 'J' and resid 10 through 14 removed outlier: 3.607A pdb=" N ALA J 88 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP J 39 " --> pdb=" O LEU J 51 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'J' and resid 10 through 14 removed outlier: 3.607A pdb=" N ALA J 88 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS J 94 " --> pdb=" O ALA J 101 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA J 101 " --> pdb=" O HIS J 94 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'J' and resid 30 through 31 Processing sheet with id=AJ1, first strand: chain 'J' and resid 118 through 122 removed outlier: 6.341A pdb=" N TYR J 177 " --> pdb=" O ASN J 142 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'J' and resid 157 through 158 1436 hydrogen bonds defined for protein. 3825 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: 30.83 Time building geometry restraints manager: 43.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 34383 1.04 - 1.23: 736 1.23 - 1.43: 14752 1.43 - 1.63: 20491 1.63 - 1.82: 207 Bond restraints: 70569 Sorted by residual: bond pdb=" C PRO A 25 " pdb=" N PRO A 26 " ideal model delta sigma weight residual 1.334 1.470 -0.136 2.34e-02 1.83e+03 3.40e+01 bond pdb=" C LEU C 229 " pdb=" N PRO C 230 " ideal model delta sigma weight residual 1.334 1.466 -0.132 2.34e-02 1.83e+03 3.19e+01 bond pdb=" C PRO C 25 " pdb=" N PRO C 26 " ideal model delta sigma weight residual 1.334 1.463 -0.129 2.34e-02 1.83e+03 3.03e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.462 -0.128 2.34e-02 1.83e+03 3.00e+01 bond pdb=" C PRO B 25 " pdb=" N PRO B 26 " ideal model delta sigma weight residual 1.334 1.455 -0.122 2.34e-02 1.83e+03 2.70e+01 ... (remaining 70564 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.17: 1468 107.17 - 113.88: 83639 113.88 - 120.59: 22479 120.59 - 127.30: 19128 127.30 - 134.02: 405 Bond angle restraints: 127119 Sorted by residual: angle pdb=" C PRO A 330 " pdb=" N ASN A 331 " pdb=" H ASN A 331 " ideal model delta sigma weight residual 123.83 107.52 16.30 3.00e+00 1.11e-01 2.95e+01 angle pdb=" N CYS B 361 " pdb=" CA CYS B 361 " pdb=" C CYS B 361 " ideal model delta sigma weight residual 110.24 103.34 6.90 1.41e+00 5.03e-01 2.40e+01 angle pdb=" N CYS C 361 " pdb=" CA CYS C 361 " pdb=" C CYS C 361 " ideal model delta sigma weight residual 110.23 103.49 6.74 1.45e+00 4.76e-01 2.16e+01 angle pdb=" CA VAL A 534 " pdb=" C VAL A 534 " pdb=" N LYS A 535 " ideal model delta sigma weight residual 116.15 121.22 -5.07 1.13e+00 7.83e-01 2.02e+01 angle pdb=" CA CYS C 361 " pdb=" C CYS C 361 " pdb=" N VAL C 362 " ideal model delta sigma weight residual 115.85 121.48 -5.63 1.29e+00 6.01e-01 1.90e+01 ... (remaining 127114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 27515 18.00 - 35.99: 273 35.99 - 53.99: 245 53.99 - 71.98: 567 71.98 - 89.98: 206 Dihedral angle restraints: 28806 sinusoidal: 12960 harmonic: 15846 Sorted by residual: dihedral pdb=" CA THR C 531 " pdb=" C THR C 531 " pdb=" N ASN C 532 " pdb=" CA ASN C 532 " ideal model delta harmonic sigma weight residual -180.00 -138.07 -41.93 0 5.00e+00 4.00e-02 7.03e+01 dihedral pdb=" CA THR B 531 " pdb=" C THR B 531 " pdb=" N ASN B 532 " pdb=" CA ASN B 532 " ideal model delta harmonic sigma weight residual -180.00 -139.02 -40.98 0 5.00e+00 4.00e-02 6.72e+01 dihedral pdb=" CA ASN A 331 " pdb=" C ASN A 331 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta harmonic sigma weight residual 180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 28803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3428 0.029 - 0.058: 1400 0.058 - 0.087: 237 0.087 - 0.116: 353 0.116 - 0.145: 120 Chirality restraints: 5538 Sorted by residual: chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE A 235 " pdb=" N ILE A 235 " pdb=" C ILE A 235 " pdb=" CB ILE A 235 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 5535 not shown) Planarity restraints: 10611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 532 " 0.137 2.00e-02 2.50e+03 1.52e-01 3.47e+02 pdb=" CG ASN C 532 " -0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN C 532 " -0.133 2.00e-02 2.50e+03 pdb=" ND2 ASN C 532 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN C 532 " -0.225 2.00e-02 2.50e+03 pdb="HD22 ASN C 532 " 0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN H 170 " 0.138 2.00e-02 2.50e+03 1.52e-01 3.44e+02 pdb=" CD GLN H 170 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN H 170 " -0.130 2.00e-02 2.50e+03 pdb=" NE2 GLN H 170 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN H 170 " -0.223 2.00e-02 2.50e+03 pdb="HE22 GLN H 170 " 0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 330 " -0.081 2.00e-02 2.50e+03 1.51e-01 2.27e+02 pdb=" N ASN A 331 " 0.260 2.00e-02 2.50e+03 pdb=" CA ASN A 331 " -0.071 2.00e-02 2.50e+03 pdb=" H ASN A 331 " -0.107 2.00e-02 2.50e+03 ... (remaining 10608 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 2000 2.16 - 2.77: 136009 2.77 - 3.38: 182588 3.38 - 3.99: 244450 3.99 - 4.60: 379717 Nonbonded interactions: 944764 Sorted by model distance: nonbonded pdb=" OE2 GLU A1031 " pdb=" HE ARG B1039 " model vdw 1.556 1.850 nonbonded pdb=" H ASN A 360 " pdb=" O THR A 393 " model vdw 1.558 1.850 nonbonded pdb=" HE ARG C1039 " pdb=" OE2 GLU B1031 " model vdw 1.562 1.850 nonbonded pdb=" OD1 ASN C1135 " pdb=" H THR C1136 " model vdw 1.562 1.850 nonbonded pdb=" OD1 ASN B 334 " pdb=" H LEU B 335 " model vdw 1.565 1.850 ... (remaining 944759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 159 5.16 5 C 22467 2.51 5 N 5898 2.21 5 O 6792 1.98 5 H 34404 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 0.760 Extract box with map and model: 13.530 Check model and map are aligned: 0.760 Process input model: 167.660 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Set scattering table: 0.650 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 191.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4174 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 0.136 36165 Z= 0.165 Angle : 0.455 7.952 49215 Z= 0.249 Chirality : 0.042 0.145 5538 Planarity : 0.003 0.084 6351 Dihedral : 7.352 79.830 12927 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.24 % Favored : 95.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.10), residues: 4476 helix: -1.75 (0.16), residues: 650 sheet: -0.59 (0.12), residues: 1377 loop : -1.34 (0.11), residues: 2449 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1165 time to evaluate : 4.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1165 average time/residue: 0.9832 time to fit residues: 1787.2783 Evaluate side-chains 641 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 641 time to evaluate : 4.416 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 377 optimal weight: 8.9990 chunk 338 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 228 optimal weight: 9.9990 chunk 181 optimal weight: 0.9980 chunk 350 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 260 optimal weight: 6.9990 chunk 405 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 360 ASN A 440 ASN A 784 GLN A 787 GLN A 901 GLN A1023 ASN A1159 HIS C 536 ASN C 787 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B1011 GLN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS H 160 GLN J 128 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4604 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 36165 Z= 0.243 Angle : 0.605 15.024 49215 Z= 0.323 Chirality : 0.045 0.199 5538 Planarity : 0.004 0.056 6351 Dihedral : 4.223 35.317 4854 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.75 % Favored : 97.18 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.81 (0.11), residues: 4476 helix: 0.54 (0.19), residues: 682 sheet: -0.05 (0.12), residues: 1357 loop : -1.13 (0.11), residues: 2437 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 654 time to evaluate : 4.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 39 residues processed: 690 average time/residue: 0.9546 time to fit residues: 1045.5390 Evaluate side-chains 574 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 535 time to evaluate : 4.130 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.7021 time to fit residues: 56.1205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 225 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 337 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 406 optimal weight: 6.9990 chunk 439 optimal weight: 7.9990 chunk 362 optimal weight: 0.6980 chunk 403 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 326 optimal weight: 7.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 207 HIS A 271 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 506 GLN C1023 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B 949 GLN ** E 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4914 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.122 36165 Z= 0.350 Angle : 0.661 14.365 49215 Z= 0.350 Chirality : 0.045 0.377 5538 Planarity : 0.005 0.061 6351 Dihedral : 4.655 32.725 4854 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.49 % Favored : 95.44 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.76 (0.12), residues: 4476 helix: 1.09 (0.19), residues: 685 sheet: -0.13 (0.13), residues: 1338 loop : -1.19 (0.11), residues: 2453 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 545 time to evaluate : 4.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 36 residues processed: 573 average time/residue: 0.9683 time to fit residues: 877.4784 Evaluate side-chains 510 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 474 time to evaluate : 4.112 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.7077 time to fit residues: 51.2070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 401 optimal weight: 8.9990 chunk 305 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 chunk 45 optimal weight: 40.0000 chunk 194 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 408 optimal weight: 3.9990 chunk 432 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 386 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 173 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4961 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 36165 Z= 0.250 Angle : 0.588 14.714 49215 Z= 0.307 Chirality : 0.044 0.221 5538 Planarity : 0.004 0.055 6351 Dihedral : 4.535 27.421 4854 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.89 % Favored : 96.05 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.12), residues: 4476 helix: 1.34 (0.19), residues: 676 sheet: -0.15 (0.13), residues: 1348 loop : -1.19 (0.11), residues: 2452 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 514 time to evaluate : 4.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 22 residues processed: 531 average time/residue: 0.9677 time to fit residues: 804.8817 Evaluate side-chains 498 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 476 time to evaluate : 4.171 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.6677 time to fit residues: 32.3793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 359 optimal weight: 8.9990 chunk 245 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 321 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 368 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 chunk 387 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN A 317 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 762 GLN C 207 HIS C 658 ASN C 755 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN B 207 HIS B 211 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5147 moved from start: 0.6793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.127 36165 Z= 0.398 Angle : 0.675 13.726 49215 Z= 0.358 Chirality : 0.045 0.175 5538 Planarity : 0.005 0.057 6351 Dihedral : 4.994 27.763 4854 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.41 % Favored : 93.50 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.12), residues: 4476 helix: 0.92 (0.19), residues: 692 sheet: -0.42 (0.14), residues: 1318 loop : -1.51 (0.11), residues: 2466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 482 time to evaluate : 4.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 38 residues processed: 512 average time/residue: 0.9868 time to fit residues: 807.9172 Evaluate side-chains 481 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 443 time to evaluate : 4.111 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.6803 time to fit residues: 52.0080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 145 optimal weight: 10.0000 chunk 389 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 432 optimal weight: 9.9990 chunk 359 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 227 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5196 moved from start: 0.7327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 36165 Z= 0.324 Angle : 0.632 14.881 49215 Z= 0.333 Chirality : 0.044 0.175 5538 Planarity : 0.004 0.052 6351 Dihedral : 5.055 27.250 4854 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.66 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.12), residues: 4476 helix: 0.96 (0.19), residues: 690 sheet: -0.64 (0.13), residues: 1348 loop : -1.64 (0.12), residues: 2438 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 463 time to evaluate : 4.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 18 residues processed: 487 average time/residue: 0.9645 time to fit residues: 748.0313 Evaluate side-chains 450 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 432 time to evaluate : 4.139 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.7104 time to fit residues: 27.8368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 416 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 246 optimal weight: 8.9990 chunk 315 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 364 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 430 optimal weight: 2.9990 chunk 269 optimal weight: 0.9980 chunk 262 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN C 658 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5138 moved from start: 0.7403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 36165 Z= 0.186 Angle : 0.562 14.266 49215 Z= 0.289 Chirality : 0.043 0.203 5538 Planarity : 0.004 0.063 6351 Dihedral : 4.735 27.350 4854 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.07 % Favored : 94.82 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.12), residues: 4476 helix: 1.51 (0.20), residues: 684 sheet: -0.53 (0.14), residues: 1351 loop : -1.46 (0.12), residues: 2441 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 456 time to evaluate : 4.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 469 average time/residue: 0.9955 time to fit residues: 743.1884 Evaluate side-chains 457 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 439 time to evaluate : 4.142 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 2 residues processed: 18 average time/residue: 0.7019 time to fit residues: 27.8681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 266 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 338 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 954 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5235 moved from start: 0.7797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 36165 Z= 0.306 Angle : 0.610 14.684 49215 Z= 0.320 Chirality : 0.043 0.167 5538 Planarity : 0.004 0.056 6351 Dihedral : 4.940 26.388 4854 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.06 % Favored : 92.83 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.12), residues: 4476 helix: 1.12 (0.20), residues: 704 sheet: -0.67 (0.13), residues: 1355 loop : -1.60 (0.12), residues: 2417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 448 time to evaluate : 4.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 21 residues processed: 464 average time/residue: 0.9745 time to fit residues: 719.0365 Evaluate side-chains 446 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 425 time to evaluate : 4.119 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 3 residues processed: 21 average time/residue: 0.6481 time to fit residues: 30.4364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 391 optimal weight: 6.9990 chunk 412 optimal weight: 0.9990 chunk 376 optimal weight: 4.9990 chunk 401 optimal weight: 8.9990 chunk 241 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 315 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 362 optimal weight: 0.9990 chunk 379 optimal weight: 9.9990 chunk 400 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B 115 GLN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5192 moved from start: 0.7874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 36165 Z= 0.200 Angle : 0.564 14.330 49215 Z= 0.290 Chirality : 0.043 0.198 5538 Planarity : 0.004 0.045 6351 Dihedral : 4.744 26.277 4854 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.76 % Favored : 94.12 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.12), residues: 4476 helix: 1.47 (0.20), residues: 698 sheet: -0.58 (0.14), residues: 1342 loop : -1.50 (0.12), residues: 2436 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 449 time to evaluate : 4.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 459 average time/residue: 0.9462 time to fit residues: 693.3193 Evaluate side-chains 438 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 429 time to evaluate : 4.140 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.7887 time to fit residues: 17.3195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 263 optimal weight: 5.9990 chunk 424 optimal weight: 4.9990 chunk 259 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 445 optimal weight: 20.0000 chunk 409 optimal weight: 3.9990 chunk 354 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5301 moved from start: 0.8283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.099 36165 Z= 0.332 Angle : 0.634 14.741 49215 Z= 0.334 Chirality : 0.044 0.166 5538 Planarity : 0.004 0.062 6351 Dihedral : 5.090 31.980 4854 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.24 % Favored : 91.64 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.12), residues: 4476 helix: 0.98 (0.19), residues: 710 sheet: -0.74 (0.14), residues: 1311 loop : -1.76 (0.12), residues: 2455 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 429 time to evaluate : 4.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 17 residues processed: 437 average time/residue: 0.9886 time to fit residues: 686.6192 Evaluate side-chains 429 residues out of total 3954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 412 time to evaluate : 4.173 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 2 residues processed: 17 average time/residue: 0.6844 time to fit residues: 26.2603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 281 optimal weight: 1.9990 chunk 377 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 326 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 355 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 364 optimal weight: 0.8980 chunk 44 optimal weight: 30.0000 chunk 65 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 856 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.140016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.113953 restraints weight = 400772.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.117304 restraints weight = 177856.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.118092 restraints weight = 92907.702| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.8277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 36165 Z= 0.177 Angle : 0.568 14.600 49215 Z= 0.291 Chirality : 0.043 0.200 5538 Planarity : 0.004 0.045 6351 Dihedral : 4.779 32.432 4854 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.39 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.12), residues: 4476 helix: 1.41 (0.20), residues: 705 sheet: -0.63 (0.13), residues: 1339 loop : -1.55 (0.12), residues: 2432 =============================================================================== Job complete usr+sys time: 14361.06 seconds wall clock time: 249 minutes 39.85 seconds (14979.85 seconds total)