Starting phenix.real_space_refine on Fri Mar 22 02:29:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wdf_32437/03_2024/7wdf_32437.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wdf_32437/03_2024/7wdf_32437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wdf_32437/03_2024/7wdf_32437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wdf_32437/03_2024/7wdf_32437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wdf_32437/03_2024/7wdf_32437.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wdf_32437/03_2024/7wdf_32437.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.124 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 145 5.16 5 C 20377 2.51 5 N 5342 2.21 5 O 6134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31998 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 2, 'PTRANS': 52, 'TRANS': 1024} Chain breaks: 8 Chain: "B" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1025} Chain breaks: 8 Chain: "C" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1025} Chain breaks: 8 Chain: "D" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "E" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Chain: "F" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "G" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 19.34, per 1000 atoms: 0.60 Number of scatterers: 31998 At special positions: 0 Unit cell: (216.414, 145.369, 202.205, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 145 16.00 O 6134 8.00 N 5342 7.00 C 20377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, 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=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 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=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 202 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 138 " - pdb=" SG CYS G 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: 15.04 Conformation dependent library (CDL) restraints added in 7.6 seconds 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7684 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 72 sheets defined 19.5% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.744A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.637A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.657A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.857A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (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: 3.727A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 5.750A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.677A 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: 3.624A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.248A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 3.988A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.611A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 737 through 743' Processing helix chain 'B' and resid 747 through 754 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: 3.502A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 4.179A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.620A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.673A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.717A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.216A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.067A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.589A 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: 3.566A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.537A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1161 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.715A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.521A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.650A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.874A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 856 removed outlier: 4.068A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.872A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.637A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.811A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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: 3.660A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.660A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.489A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.981A pdb=" N PHE D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.542A pdb=" N SER D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 removed outlier: 3.923A pdb=" N SER D 197 " --> pdb=" O SER D 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.752A pdb=" N ALA E 87 " --> pdb=" O GLU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 removed outlier: 3.529A pdb=" N SER E 131 " --> pdb=" O GLU E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.559A pdb=" N SER F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.680A pdb=" N ALA G 87 " --> pdb=" O GLU G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 132 Processing helix chain 'G' and resid 187 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.108A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.128A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.164A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.494A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.501A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.852A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.506A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.644A pdb=" N LYS A 424 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU A 465 " --> pdb=" O LYS A 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.438A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.757A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.080A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 6.899A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 7.327A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.613A pdb=" N GLY B 142 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.738A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 327 Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.758A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 423 through 424 removed outlier: 3.824A pdb=" N GLU B 465 " --> pdb=" O LYS B 424 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.339A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.624A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.648A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.292A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.205A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.071A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.566A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.564A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.531A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 423 through 424 removed outlier: 3.563A pdb=" N LYS C 424 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU C 465 " --> pdb=" O LYS C 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.180A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 727 removed outlier: 3.882A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.348A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AF5, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.806A pdb=" N MET D 34 " --> pdb=" O MET D 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N MET D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.606A pdb=" N CYS D 96 " --> pdb=" O TRP D 110 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TRP D 110 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARG D 98 " --> pdb=" O ALA D 108 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 127 through 131 removed outlier: 3.572A pdb=" N GLY D 151 " --> pdb=" O TYR D 182 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR D 182 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 127 through 131 removed outlier: 3.572A pdb=" N GLY D 151 " --> pdb=" O TYR D 182 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR D 182 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AG1, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.520A pdb=" N SER E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP E 74 " --> pdb=" O SER E 71 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.465A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS E 111 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL E 13 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TRP E 39 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.465A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS E 111 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL E 13 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS E 94 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA E 101 " --> pdb=" O HIS E 94 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 30 through 31 Processing sheet with id=AG5, first strand: chain 'E' and resid 118 through 122 removed outlier: 5.952A pdb=" N TYR E 177 " --> pdb=" O ASN E 142 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 157 through 158 Processing sheet with id=AG7, first strand: chain 'F' and resid 3 through 5 Processing sheet with id=AG8, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.830A pdb=" N MET F 34 " --> pdb=" O MET F 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG F 40 " --> pdb=" O GLY F 44 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.661A pdb=" N CYS F 96 " --> pdb=" O TRP F 110 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TRP F 110 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ARG F 98 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA F 108 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 127 through 131 removed outlier: 6.538A pdb=" N TYR F 182 " --> pdb=" O GLY F 151 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 127 through 131 removed outlier: 6.538A pdb=" N TYR F 182 " --> pdb=" O GLY F 151 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 158 through 161 removed outlier: 4.056A pdb=" N VAL F 200 " --> pdb=" O ILE F 217 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AH5, first strand: chain 'G' and resid 10 through 14 removed outlier: 6.496A pdb=" N LEU G 11 " --> pdb=" O GLU G 109 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS G 111 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL G 13 " --> pdb=" O LYS G 111 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE G 52 " --> pdb=" O TRP G 39 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN G 41 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU G 50 " --> pdb=" O GLN G 41 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 14 removed outlier: 6.496A pdb=" N LEU G 11 " --> pdb=" O GLU G 109 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS G 111 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL G 13 " --> pdb=" O LYS G 111 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA G 101 " --> pdb=" O HIS G 94 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 30 through 31 Processing sheet with id=AH8, first strand: chain 'G' and resid 118 through 122 removed outlier: 6.047A pdb=" N TYR G 177 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 157 through 159 removed outlier: 4.366A pdb=" N TRP G 152 " --> pdb=" O ARG G 159 " (cutoff:3.500A) 1309 hydrogen bonds defined for protein. 3528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.38 Time building geometry restraints manager: 16.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 10288 1.35 - 1.46: 8072 1.46 - 1.58: 14212 1.58 - 1.70: 0 1.70 - 1.82: 187 Bond restraints: 32759 Sorted by residual: bond pdb=" C CYS A 336 " pdb=" N PRO A 337 " ideal model delta sigma weight residual 1.334 1.468 -0.135 2.34e-02 1.83e+03 3.30e+01 bond pdb=" C CYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.456 -0.122 2.34e-02 1.83e+03 2.72e+01 bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.432 -0.098 2.34e-02 1.83e+03 1.75e+01 bond pdb=" C CYS C 336 " pdb=" N PRO C 337 " ideal model delta sigma weight residual 1.334 1.408 -0.074 2.34e-02 1.83e+03 9.98e+00 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.406 -0.072 2.34e-02 1.83e+03 9.50e+00 ... (remaining 32754 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.18: 1060 107.18 - 113.91: 18214 113.91 - 120.64: 12607 120.64 - 127.37: 12343 127.37 - 134.10: 345 Bond angle restraints: 44569 Sorted by residual: angle pdb=" C VAL A 534 " pdb=" N LYS A 535 " pdb=" CA LYS A 535 " ideal model delta sigma weight residual 121.70 129.48 -7.78 1.80e+00 3.09e-01 1.87e+01 angle pdb=" C CYS C 361 " pdb=" N VAL C 362 " pdb=" CA VAL C 362 " ideal model delta sigma weight residual 121.70 129.27 -7.57 1.80e+00 3.09e-01 1.77e+01 angle pdb=" CA CYS C 361 " pdb=" C CYS C 361 " pdb=" N VAL C 362 " ideal model delta sigma weight residual 115.85 121.21 -5.36 1.29e+00 6.01e-01 1.73e+01 angle pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta sigma weight residual 121.70 129.03 -7.33 1.80e+00 3.09e-01 1.66e+01 angle pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " ideal model delta sigma weight residual 115.85 120.85 -5.00 1.29e+00 6.01e-01 1.50e+01 ... (remaining 44564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 19050 16.67 - 33.34: 322 33.34 - 50.01: 112 50.01 - 66.68: 25 66.68 - 83.35: 6 Dihedral angle restraints: 19515 sinusoidal: 7577 harmonic: 11938 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 -149.28 -30.72 0 5.00e+00 4.00e-02 3.77e+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 -150.09 -29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA TYR D 101 " pdb=" C TYR D 101 " pdb=" N ASP D 102 " pdb=" CA ASP D 102 " ideal model delta harmonic sigma weight residual 180.00 153.68 26.32 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 19512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3183 0.030 - 0.060: 1178 0.060 - 0.090: 291 0.090 - 0.120: 338 0.120 - 0.150: 29 Chirality restraints: 5019 Sorted by residual: chirality pdb=" CA ILE C 714 " pdb=" N ILE C 714 " pdb=" C ILE C 714 " pdb=" CB ILE C 714 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA ILE B 714 " pdb=" N ILE B 714 " pdb=" C ILE B 714 " pdb=" CB ILE B 714 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE G 148 " pdb=" N ILE G 148 " pdb=" C ILE G 148 " pdb=" CB ILE G 148 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 5016 not shown) Planarity restraints: 5758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO C 986 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 985 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO B 986 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 986 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 986 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.021 5.00e-02 4.00e+02 3.11e-02 1.54e+00 pdb=" N PRO A 986 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.017 5.00e-02 4.00e+02 ... (remaining 5755 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1017 2.72 - 3.26: 30479 3.26 - 3.81: 50757 3.81 - 4.35: 64017 4.35 - 4.90: 109160 Nonbonded interactions: 255430 Sorted by model distance: nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.170 2.440 nonbonded pdb=" O ASP G 86 " pdb=" OH TYR G 90 " model vdw 2.214 2.440 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.215 2.440 nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.218 2.440 nonbonded pdb=" O ILE A 742 " pdb=" NH1 ARG A1000 " model vdw 2.242 2.520 ... (remaining 255425 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 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.410 Check model and map are aligned: 0.460 Set scattering table: 0.360 Process input model: 96.110 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4089 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 : 0.002 0.135 32759 Z= 0.142 Angle : 0.514 7.783 44569 Z= 0.295 Chirality : 0.042 0.150 5019 Planarity : 0.002 0.032 5758 Dihedral : 7.628 83.354 11708 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.27 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.73 (0.11), residues: 4048 helix: -2.52 (0.13), residues: 663 sheet: -0.30 (0.13), residues: 1168 loop : -1.12 (0.11), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.004 0.000 HIS G 38 PHE 0.018 0.001 PHE C 490 TYR 0.020 0.001 TYR B 501 ARG 0.002 0.000 ARG G 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1051 time to evaluate : 3.652 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: A 699 LEU cc_start: 0.6491 (mt) cc_final: 0.6281 (mt) REVERT: B 177 MET cc_start: -0.2333 (ttp) cc_final: -0.3229 (mmt) REVERT: B 293 LEU cc_start: 0.6839 (tp) cc_final: 0.6637 (tp) REVERT: C 534 VAL cc_start: 0.6460 (m) cc_final: 0.6101 (m) outliers start: 0 outliers final: 0 residues processed: 1051 average time/residue: 0.4555 time to fit residues: 741.4297 Evaluate side-chains 518 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 518 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 341 optimal weight: 9.9990 chunk 306 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 104 optimal weight: 0.3980 chunk 207 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 317 optimal weight: 0.4980 chunk 122 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 367 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 148 ASN A 239 GLN A 394 ASN ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 613 GLN A 644 GLN A 751 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 787 GLN B 895 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1002 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 239 GLN C 487 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN C1142 GLN D 178 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN F 82 GLN G 128 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4506 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32759 Z= 0.187 Angle : 0.645 13.564 44569 Z= 0.330 Chirality : 0.046 0.279 5019 Planarity : 0.004 0.057 5758 Dihedral : 4.475 34.165 4389 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.52 % Favored : 97.43 % Rotamer: Outliers : 2.37 % Allowed : 9.89 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % 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: -0.62 (0.12), residues: 4048 helix: 0.29 (0.19), residues: 676 sheet: 0.22 (0.14), residues: 1113 loop : -0.95 (0.12), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 110 HIS 0.009 0.001 HIS F 52 PHE 0.043 0.002 PHE C 855 TYR 0.022 0.002 TYR B1155 ARG 0.010 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 564 time to evaluate : 3.939 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: A 177 MET cc_start: 0.1651 (mmt) cc_final: 0.1242 (mmm) REVERT: A 314 GLN cc_start: 0.7860 (tp-100) cc_final: 0.7513 (tm-30) REVERT: A 708 SER cc_start: 0.6709 (t) cc_final: 0.6501 (m) REVERT: A 957 GLN cc_start: 0.6262 (tt0) cc_final: 0.6030 (tt0) REVERT: B 177 MET cc_start: -0.2123 (ttp) cc_final: -0.3013 (mmt) REVERT: B 533 LEU cc_start: 0.4045 (tt) cc_final: 0.3408 (tp) REVERT: C 429 PHE cc_start: 0.1635 (t80) cc_final: 0.0971 (t80) REVERT: C 955 ASN cc_start: 0.6968 (m-40) cc_final: 0.5706 (m-40) REVERT: C 1014 ARG cc_start: 0.6570 (mmm-85) cc_final: 0.6180 (mmm-85) outliers start: 85 outliers final: 53 residues processed: 612 average time/residue: 0.4514 time to fit residues: 437.6433 Evaluate side-chains 489 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 436 time to evaluate : 3.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain G residue 82 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 204 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 306 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 368 optimal weight: 0.9980 chunk 398 optimal weight: 1.9990 chunk 328 optimal weight: 0.9980 chunk 365 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 295 optimal weight: 0.5980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 856 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 321 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 913 GLN B 925 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 360 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4756 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 32759 Z= 0.227 Angle : 0.621 10.670 44569 Z= 0.320 Chirality : 0.045 0.199 5019 Planarity : 0.004 0.051 5758 Dihedral : 4.510 31.139 4389 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.96 % Rotamer: Outliers : 3.02 % Allowed : 10.84 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % 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: -0.35 (0.12), residues: 4048 helix: 0.74 (0.19), residues: 690 sheet: 0.37 (0.14), residues: 1126 loop : -0.86 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 36 HIS 0.012 0.001 HIS C1048 PHE 0.029 0.002 PHE B1109 TYR 0.020 0.002 TYR B1155 ARG 0.012 0.001 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 466 time to evaluate : 3.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1991 (mmp) cc_final: 0.1708 (mmm) REVERT: A 708 SER cc_start: 0.6888 (t) cc_final: 0.6614 (m) REVERT: B 119 ILE cc_start: 0.4537 (pt) cc_final: 0.4155 (pt) REVERT: B 177 MET cc_start: -0.2199 (ttp) cc_final: -0.2839 (mmt) REVERT: B 1014 ARG cc_start: 0.6735 (tpp80) cc_final: 0.6481 (tpp80) REVERT: C 965 GLN cc_start: 0.6767 (tp40) cc_final: 0.6447 (tp40) REVERT: C 1014 ARG cc_start: 0.6459 (mmm-85) cc_final: 0.6171 (mmm-85) REVERT: F 98 ARG cc_start: 0.1239 (OUTLIER) cc_final: 0.0540 (mmm-85) REVERT: F 177 LEU cc_start: 0.4965 (OUTLIER) cc_final: 0.4737 (mp) outliers start: 108 outliers final: 77 residues processed: 535 average time/residue: 0.4168 time to fit residues: 362.1321 Evaluate side-chains 470 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 391 time to evaluate : 4.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 817 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain G residue 82 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 364 optimal weight: 30.0000 chunk 277 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 175 optimal weight: 0.0040 chunk 247 optimal weight: 10.0000 chunk 369 optimal weight: 4.9990 chunk 391 optimal weight: 10.0000 chunk 193 optimal weight: 0.9980 chunk 350 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 overall best weight: 2.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 762 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 544 ASN C 564 GLN C 607 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1005 GLN C1159 HIS ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4967 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 32759 Z= 0.277 Angle : 0.648 12.503 44569 Z= 0.335 Chirality : 0.045 0.258 5019 Planarity : 0.004 0.079 5758 Dihedral : 4.722 32.883 4389 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 3.21 % Allowed : 12.15 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % 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: -0.45 (0.12), residues: 4048 helix: 0.85 (0.19), residues: 698 sheet: 0.20 (0.14), residues: 1137 loop : -0.94 (0.12), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 886 HIS 0.007 0.001 HIS E 80 PHE 0.024 0.002 PHE C 306 TYR 0.024 0.002 TYR B 695 ARG 0.020 0.001 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 419 time to evaluate : 3.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.2071 (mmp) cc_final: 0.1705 (mmm) REVERT: A 568 ASP cc_start: 0.4987 (p0) cc_final: 0.4700 (p0) REVERT: A 708 SER cc_start: 0.7052 (t) cc_final: 0.6723 (m) REVERT: A 779 GLN cc_start: 0.6627 (mt0) cc_final: 0.6413 (mt0) REVERT: A 945 LEU cc_start: 0.7473 (mt) cc_final: 0.7271 (mp) REVERT: A 1017 GLU cc_start: 0.6288 (tp30) cc_final: 0.6040 (tm-30) REVERT: B 177 MET cc_start: -0.2042 (ttp) cc_final: -0.2758 (mmp) REVERT: B 1010 GLN cc_start: 0.5684 (OUTLIER) cc_final: 0.5468 (tt0) REVERT: B 1029 MET cc_start: 0.6870 (tpp) cc_final: 0.6369 (ttp) REVERT: C 177 MET cc_start: 0.0955 (mtp) cc_final: 0.0536 (mtm) REVERT: C 965 GLN cc_start: 0.6544 (tp40) cc_final: 0.6212 (tp40) REVERT: F 177 LEU cc_start: 0.5150 (OUTLIER) cc_final: 0.4935 (mp) outliers start: 115 outliers final: 83 residues processed: 493 average time/residue: 0.4198 time to fit residues: 339.7433 Evaluate side-chains 458 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 373 time to evaluate : 3.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 184 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 326 optimal weight: 8.9990 chunk 222 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 291 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 334 optimal weight: 0.1980 chunk 270 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 0.7980 chunk 351 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 762 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 751 ASN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN C 414 GLN C 613 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 GLN ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5212 moved from start: 0.6631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 32759 Z= 0.374 Angle : 0.740 13.345 44569 Z= 0.386 Chirality : 0.048 0.265 5019 Planarity : 0.005 0.056 5758 Dihedral : 5.297 38.802 4389 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 22.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.03 % Favored : 95.92 % Rotamer: Outliers : 3.83 % Allowed : 13.13 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % 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: -0.76 (0.12), residues: 4048 helix: 0.67 (0.19), residues: 716 sheet: 0.00 (0.15), residues: 1131 loop : -1.18 (0.12), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 886 HIS 0.009 0.002 HIS A 207 PHE 0.029 0.003 PHE A1042 TYR 0.028 0.002 TYR B 695 ARG 0.008 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 385 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1880 (mmp) cc_final: 0.0347 (mtp) REVERT: A 1017 GLU cc_start: 0.6461 (tp30) cc_final: 0.6212 (tm-30) REVERT: A 1148 PHE cc_start: 0.4101 (OUTLIER) cc_final: 0.2960 (m-10) REVERT: B 177 MET cc_start: -0.2076 (ttp) cc_final: -0.2851 (mmt) REVERT: B 302 THR cc_start: 0.7969 (OUTLIER) cc_final: 0.7748 (t) REVERT: B 1029 MET cc_start: 0.7033 (tpp) cc_final: 0.6785 (tpp) REVERT: C 177 MET cc_start: 0.1706 (mtp) cc_final: 0.0699 (mtm) REVERT: C 304 LYS cc_start: 0.8016 (mmtm) cc_final: 0.7803 (mmtt) outliers start: 137 outliers final: 103 residues processed: 483 average time/residue: 0.3963 time to fit residues: 316.7820 Evaluate side-chains 447 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 342 time to evaluate : 3.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 777 ASN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain G residue 5 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 131 optimal weight: 0.9990 chunk 352 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 229 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 391 optimal weight: 6.9990 chunk 325 optimal weight: 0.0070 chunk 181 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- 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 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 644 GLN C 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5157 moved from start: 0.6818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 32759 Z= 0.229 Angle : 0.648 14.084 44569 Z= 0.330 Chirality : 0.045 0.314 5019 Planarity : 0.004 0.065 5758 Dihedral : 5.011 38.647 4389 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 3.49 % Allowed : 14.58 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % 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: -0.72 (0.12), residues: 4048 helix: 0.81 (0.19), residues: 723 sheet: 0.09 (0.15), residues: 1105 loop : -1.23 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 886 HIS 0.008 0.001 HIS E 93 PHE 0.035 0.002 PHE A 497 TYR 0.020 0.002 TYR C1138 ARG 0.006 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 381 time to evaluate : 3.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.2009 (mmp) cc_final: 0.0550 (mtp) REVERT: A 761 THR cc_start: 0.6949 (OUTLIER) cc_final: 0.6551 (m) REVERT: A 762 GLN cc_start: 0.5486 (tp40) cc_final: 0.4697 (tp-100) REVERT: A 1148 PHE cc_start: 0.4153 (OUTLIER) cc_final: 0.2931 (m-10) REVERT: B 177 MET cc_start: -0.1906 (ttp) cc_final: -0.2739 (mmt) REVERT: B 306 PHE cc_start: 0.5157 (OUTLIER) cc_final: 0.4887 (m-10) REVERT: B 1029 MET cc_start: 0.6935 (tpp) cc_final: 0.6733 (tpp) REVERT: C 177 MET cc_start: 0.2459 (mtp) cc_final: 0.1556 (mtm) REVERT: D 142 MET cc_start: 0.4667 (tmm) cc_final: 0.4319 (tmm) outliers start: 125 outliers final: 94 residues processed: 466 average time/residue: 0.4011 time to fit residues: 309.2672 Evaluate side-chains 446 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 349 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 177 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 377 optimal weight: 9.9990 chunk 44 optimal weight: 0.5980 chunk 223 optimal weight: 20.0000 chunk 286 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 329 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 390 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 237 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 245 HIS ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5337 moved from start: 0.7642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 32759 Z= 0.358 Angle : 0.751 14.903 44569 Z= 0.386 Chirality : 0.048 0.317 5019 Planarity : 0.005 0.076 5758 Dihedral : 5.508 42.713 4389 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 25.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.24 % Rotamer: Outliers : 3.94 % Allowed : 14.44 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % 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: -1.00 (0.12), residues: 4048 helix: 0.57 (0.18), residues: 713 sheet: -0.09 (0.15), residues: 1112 loop : -1.41 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 886 HIS 0.008 0.002 HIS E 93 PHE 0.033 0.002 PHE A 497 TYR 0.024 0.002 TYR C1138 ARG 0.010 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 366 time to evaluate : 3.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1964 (mmp) cc_final: 0.0457 (mtp) REVERT: A 1148 PHE cc_start: 0.4269 (OUTLIER) cc_final: 0.3628 (m-80) REVERT: B 141 LEU cc_start: 0.5337 (OUTLIER) cc_final: 0.5095 (tp) REVERT: B 177 MET cc_start: -0.1630 (ttp) cc_final: -0.2480 (mmt) REVERT: B 306 PHE cc_start: 0.5256 (OUTLIER) cc_final: 0.4913 (m-10) REVERT: B 380 TYR cc_start: 0.5472 (OUTLIER) cc_final: 0.4148 (m-10) REVERT: B 1019 ARG cc_start: 0.7331 (tpt90) cc_final: 0.6952 (tpt170) REVERT: C 177 MET cc_start: 0.2913 (mtp) cc_final: 0.2395 (mtm) REVERT: C 774 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6753 (mt0) REVERT: C 969 ASN cc_start: 0.6486 (m-40) cc_final: 0.6184 (m110) outliers start: 141 outliers final: 114 residues processed: 468 average time/residue: 0.4149 time to fit residues: 320.0012 Evaluate side-chains 450 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 331 time to evaluate : 3.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 777 ASN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 5 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 241 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 233 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 265 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 306 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 955 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5239 moved from start: 0.7719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32759 Z= 0.222 Angle : 0.676 13.408 44569 Z= 0.342 Chirality : 0.046 0.324 5019 Planarity : 0.004 0.081 5758 Dihedral : 5.174 40.569 4389 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 3.27 % Allowed : 15.81 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % 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: -0.86 (0.13), residues: 4048 helix: 0.75 (0.19), residues: 716 sheet: -0.03 (0.15), residues: 1116 loop : -1.33 (0.12), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 886 HIS 0.007 0.001 HIS E 93 PHE 0.029 0.002 PHE A 497 TYR 0.028 0.002 TYR F 101 ARG 0.009 0.001 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 365 time to evaluate : 3.825 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: A 177 MET cc_start: 0.1898 (mmp) cc_final: 0.0493 (mtp) REVERT: A 1148 PHE cc_start: 0.4286 (OUTLIER) cc_final: 0.4020 (m-80) REVERT: B 176 LEU cc_start: -0.2527 (OUTLIER) cc_final: -0.2738 (pp) REVERT: B 177 MET cc_start: -0.1407 (ttp) cc_final: -0.2419 (mmt) REVERT: B 1019 ARG cc_start: 0.7263 (tpt90) cc_final: 0.6993 (tpt170) REVERT: C 177 MET cc_start: 0.2669 (mtp) cc_final: 0.2136 (mtm) REVERT: C 969 ASN cc_start: 0.6275 (m-40) cc_final: 0.6021 (m110) REVERT: C 1005 GLN cc_start: 0.5743 (tm-30) cc_final: 0.5529 (tm-30) outliers start: 117 outliers final: 94 residues processed: 447 average time/residue: 0.4290 time to fit residues: 315.1489 Evaluate side-chains 431 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 335 time to evaluate : 4.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 5 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 355 optimal weight: 9.9990 chunk 373 optimal weight: 10.0000 chunk 341 optimal weight: 20.0000 chunk 363 optimal weight: 0.9990 chunk 218 optimal weight: 8.9990 chunk 158 optimal weight: 0.7980 chunk 285 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 328 optimal weight: 2.9990 chunk 344 optimal weight: 7.9990 chunk 362 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 926 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 955 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5289 moved from start: 0.7981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 32759 Z= 0.258 Angle : 0.698 12.776 44569 Z= 0.354 Chirality : 0.047 0.281 5019 Planarity : 0.005 0.159 5758 Dihedral : 5.240 40.294 4389 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.99 % Favored : 94.96 % Rotamer: Outliers : 3.21 % Allowed : 16.37 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % 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: -0.97 (0.13), residues: 4048 helix: 0.63 (0.19), residues: 722 sheet: -0.13 (0.15), residues: 1120 loop : -1.38 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 886 HIS 0.007 0.001 HIS E 93 PHE 0.043 0.002 PHE B 306 TYR 0.041 0.002 TYR F 101 ARG 0.008 0.001 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 351 time to evaluate : 3.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.2068 (mmp) cc_final: 0.0667 (mtp) REVERT: A 761 THR cc_start: 0.7129 (OUTLIER) cc_final: 0.6441 (m) REVERT: A 822 LEU cc_start: 0.6147 (mp) cc_final: 0.5863 (mp) REVERT: A 1148 PHE cc_start: 0.4483 (OUTLIER) cc_final: 0.3838 (m-80) REVERT: B 141 LEU cc_start: 0.5285 (OUTLIER) cc_final: 0.5044 (tp) REVERT: B 176 LEU cc_start: -0.2277 (OUTLIER) cc_final: -0.2590 (pp) REVERT: B 177 MET cc_start: -0.1277 (ttp) cc_final: -0.2359 (mmt) REVERT: B 380 TYR cc_start: 0.5326 (OUTLIER) cc_final: 0.3977 (m-10) REVERT: B 1019 ARG cc_start: 0.7144 (tpt90) cc_final: 0.6868 (tpt170) REVERT: C 177 MET cc_start: 0.2890 (mtp) cc_final: 0.2302 (mtm) REVERT: C 752 LEU cc_start: 0.7534 (mt) cc_final: 0.7231 (mp) REVERT: C 869 MET cc_start: 0.7081 (mtp) cc_final: 0.6823 (mtp) REVERT: C 969 ASN cc_start: 0.6294 (m-40) cc_final: 0.6046 (m110) outliers start: 115 outliers final: 100 residues processed: 432 average time/residue: 0.4017 time to fit residues: 284.6963 Evaluate side-chains 443 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 338 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 151 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 238 optimal weight: 5.9990 chunk 384 optimal weight: 0.8980 chunk 234 optimal weight: 0.4980 chunk 182 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 403 optimal weight: 6.9990 chunk 371 optimal weight: 6.9990 chunk 321 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 955 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5231 moved from start: 0.8032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32759 Z= 0.202 Angle : 0.683 13.611 44569 Z= 0.342 Chirality : 0.046 0.312 5019 Planarity : 0.005 0.138 5758 Dihedral : 5.095 38.487 4389 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.56 % Favored : 96.42 % Rotamer: Outliers : 2.82 % Allowed : 16.90 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % 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: -0.87 (0.13), residues: 4048 helix: 0.69 (0.19), residues: 721 sheet: -0.02 (0.15), residues: 1080 loop : -1.31 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 886 HIS 0.006 0.001 HIS E 93 PHE 0.041 0.002 PHE C 559 TYR 0.043 0.002 TYR B1007 ARG 0.010 0.001 ARG A 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 356 time to evaluate : 3.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.2053 (mmp) cc_final: 0.0684 (mtp) REVERT: A 822 LEU cc_start: 0.6222 (mp) cc_final: 0.5940 (mp) REVERT: A 1148 PHE cc_start: 0.4327 (OUTLIER) cc_final: 0.3700 (m-80) REVERT: B 176 LEU cc_start: -0.2012 (OUTLIER) cc_final: -0.2459 (pp) REVERT: B 177 MET cc_start: -0.1326 (ttp) cc_final: -0.2450 (mmt) REVERT: B 380 TYR cc_start: 0.5143 (OUTLIER) cc_final: 0.3809 (m-10) REVERT: B 1019 ARG cc_start: 0.7175 (tpt90) cc_final: 0.6774 (tpt170) REVERT: C 177 MET cc_start: 0.3148 (mtp) cc_final: 0.2378 (mtt) REVERT: C 762 GLN cc_start: 0.5400 (OUTLIER) cc_final: 0.5143 (pt0) REVERT: C 969 ASN cc_start: 0.6234 (m-40) cc_final: 0.5963 (m110) outliers start: 101 outliers final: 86 residues processed: 427 average time/residue: 0.4139 time to fit residues: 289.8825 Evaluate side-chains 424 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 334 time to evaluate : 3.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 255 optimal weight: 6.9990 chunk 342 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 296 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 321 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 330 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 926 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 955 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.121537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.095734 restraints weight = 159390.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.097651 restraints weight = 84850.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.098919 restraints weight = 54414.786| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.8289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 32759 Z= 0.268 Angle : 0.704 11.846 44569 Z= 0.357 Chirality : 0.047 0.430 5019 Planarity : 0.005 0.137 5758 Dihedral : 5.208 38.692 4389 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 2.91 % Allowed : 16.98 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % 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: -0.96 (0.13), residues: 4048 helix: 0.57 (0.19), residues: 727 sheet: -0.09 (0.15), residues: 1100 loop : -1.35 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 886 HIS 0.005 0.001 HIS E 93 PHE 0.029 0.002 PHE B 306 TYR 0.057 0.002 TYR B1007 ARG 0.016 0.001 ARG A 995 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7582.58 seconds wall clock time: 137 minutes 33.84 seconds (8253.84 seconds total)