Starting phenix.real_space_refine on Fri Mar 6 14:11:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wdf_32437/03_2026/7wdf_32437.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wdf_32437/03_2026/7wdf_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wdf_32437/03_2026/7wdf_32437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wdf_32437/03_2026/7wdf_32437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wdf_32437/03_2026/7wdf_32437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wdf_32437/03_2026/7wdf_32437.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 6.46, per 1000 atoms: 0.20 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 - 3.00 Amino acid : True - 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: 2.85 Conformation dependent library (CDL) restraints added in 1.3 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: 1.41 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: 8.53 Time building geometry restraints manager: 3.86 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: 0.00 - 1.56: 43850 1.56 - 3.11: 564 3.11 - 4.67: 124 4.67 - 6.23: 15 6.23 - 7.78: 16 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 3.040 nonbonded pdb=" O ASP G 86 " pdb=" OH TYR G 90 " model vdw 2.214 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.218 3.040 nonbonded pdb=" O ILE A 742 " pdb=" NH1 ARG A1000 " model vdw 2.242 3.120 ... (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 Time spend for trying shortcut: 0.03 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: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 31.310 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.570 ------------------------------------------------------------------------------- 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 32800 Z= 0.115 Angle : 0.514 7.783 44651 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 : 7.44 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG G 96 TYR 0.020 0.001 TYR B 501 PHE 0.018 0.001 PHE C 490 TRP 0.015 0.001 TRP A 64 HIS 0.004 0.000 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00220 (32759) covalent geometry : angle 0.51369 (44569) SS BOND : bond 0.00277 ( 41) SS BOND : angle 0.72619 ( 82) hydrogen bonds : bond 0.23849 ( 1260) hydrogen bonds : angle 9.92792 ( 3528) *********************** 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 to be fit. rotamer outliers: 0 poor density : 1051 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.6491 (mt) cc_final: 0.6284 (mt) REVERT: B 177 MET cc_start: -0.2333 (ttp) cc_final: -0.3130 (mmt) REVERT: B 293 LEU cc_start: 0.6839 (tp) cc_final: 0.6633 (tp) REVERT: C 534 VAL cc_start: 0.6460 (m) cc_final: 0.6055 (m) outliers start: 0 outliers final: 0 residues processed: 1051 average time/residue: 0.2090 time to fit residues: 343.3193 Evaluate side-chains 514 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 514 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 644 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 913 GLN A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 532 ASN B 655 HIS B 787 GLN B 895 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 955 ASN B1002 GLN B1071 GLN C 207 HIS C 239 GLN C 487 ASN C 762 GLN C 787 GLN C 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN C1142 GLN D 178 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN F 82 GLN F 112 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.144008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.124268 restraints weight = 176583.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.126096 restraints weight = 101636.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.126978 restraints weight = 55108.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.127047 restraints weight = 43861.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.127195 restraints weight = 41287.654| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32800 Z= 0.150 Angle : 0.677 13.878 44651 Z= 0.348 Chirality : 0.047 0.249 5019 Planarity : 0.004 0.058 5758 Dihedral : 4.599 33.626 4389 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.40 % Favored : 97.55 % Rotamer: Outliers : 2.37 % Allowed : 10.03 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.12), residues: 4048 helix: 0.13 (0.18), residues: 682 sheet: 0.19 (0.14), residues: 1088 loop : -0.94 (0.12), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 457 TYR 0.029 0.002 TYR B 145 PHE 0.041 0.002 PHE C 855 TRP 0.026 0.002 TRP D 110 HIS 0.007 0.001 HIS F 52 Details of bonding type rmsd covalent geometry : bond 0.00324 (32759) covalent geometry : angle 0.67520 (44569) SS BOND : bond 0.00477 ( 41) SS BOND : angle 1.28945 ( 82) hydrogen bonds : bond 0.04896 ( 1260) hydrogen bonds : angle 6.70937 ( 3528) *********************** 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 638 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 553 time to evaluate : 1.199 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: A 153 MET cc_start: 0.2830 (ppp) cc_final: 0.2244 (pmm) REVERT: A 177 MET cc_start: 0.0796 (mmt) cc_final: 0.0275 (mmm) REVERT: A 239 GLN cc_start: 0.8516 (mt0) cc_final: 0.8217 (tp40) REVERT: A 287 ASP cc_start: 0.8728 (t0) cc_final: 0.8475 (t70) REVERT: A 316 SER cc_start: 0.8991 (t) cc_final: 0.8538 (m) REVERT: A 708 SER cc_start: 0.8404 (t) cc_final: 0.7729 (m) REVERT: A 773 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8150 (mm-30) REVERT: A 900 MET cc_start: 0.7553 (mtt) cc_final: 0.6916 (mtp) REVERT: A 995 ARG cc_start: 0.8998 (mtp85) cc_final: 0.8720 (mtp85) REVERT: A 1042 PHE cc_start: 0.9077 (t80) cc_final: 0.8768 (t80) REVERT: B 55 PHE cc_start: 0.7420 (m-10) cc_final: 0.7145 (m-10) REVERT: B 128 ILE cc_start: 0.9052 (mm) cc_final: 0.8750 (mm) REVERT: B 177 MET cc_start: 0.0448 (ttp) cc_final: -0.0772 (mmt) REVERT: B 533 LEU cc_start: 0.5746 (tt) cc_final: 0.5304 (tp) REVERT: B 765 ARG cc_start: 0.8556 (ptm160) cc_final: 0.8311 (ptp90) REVERT: B 773 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7946 (mm-30) REVERT: B 858 LEU cc_start: 0.8407 (mm) cc_final: 0.8064 (tp) REVERT: B 928 ASN cc_start: 0.8640 (m-40) cc_final: 0.8380 (m-40) REVERT: B 955 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7830 (t0) REVERT: B 995 ARG cc_start: 0.8871 (mtm-85) cc_final: 0.8399 (mtm-85) REVERT: B 1111 GLU cc_start: 0.7910 (tt0) cc_final: 0.7435 (pp20) REVERT: C 54 LEU cc_start: 0.8590 (tp) cc_final: 0.8385 (tp) REVERT: C 195 LYS cc_start: 0.8833 (pttm) cc_final: 0.7992 (ptmm) REVERT: C 429 PHE cc_start: 0.3232 (t80) cc_final: 0.2206 (t80) REVERT: C 489 TYR cc_start: 0.6133 (m-10) cc_final: 0.4619 (m-80) REVERT: C 564 GLN cc_start: 0.8528 (mt0) cc_final: 0.8035 (tp-100) REVERT: C 732 THR cc_start: 0.9304 (m) cc_final: 0.8903 (p) REVERT: C 772 VAL cc_start: 0.9356 (t) cc_final: 0.9138 (m) REVERT: C 773 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8021 (mm-30) REVERT: C 780 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6787 (mt-10) REVERT: C 859 THR cc_start: 0.8815 (m) cc_final: 0.8379 (p) REVERT: C 955 ASN cc_start: 0.9101 (m-40) cc_final: 0.7556 (m-40) REVERT: C 965 GLN cc_start: 0.8990 (tp40) cc_final: 0.7901 (tp-100) REVERT: C 991 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8357 (p) REVERT: C 995 ARG cc_start: 0.9087 (mtt180) cc_final: 0.8833 (mtm180) REVERT: C 1014 ARG cc_start: 0.8862 (mmm-85) cc_final: 0.8552 (mmm-85) REVERT: C 1146 ASP cc_start: 0.8838 (t70) cc_final: 0.8581 (m-30) REVERT: D 36 TRP cc_start: 0.6039 (m100) cc_final: 0.5541 (m100) REVERT: D 63 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8706 (ptpt) REVERT: D 178 GLN cc_start: 0.5515 (OUTLIER) cc_final: 0.5112 (pm20) REVERT: F 36 TRP cc_start: 0.6583 (m100) cc_final: 0.6262 (m100) REVERT: F 46 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7689 (pm20) REVERT: F 64 PHE cc_start: 0.8617 (m-80) cc_final: 0.8231 (m-10) REVERT: G 49 LYS cc_start: 0.7933 (pttm) cc_final: 0.7213 (mmtm) REVERT: G 96 ARG cc_start: 0.7838 (tpt-90) cc_final: 0.7217 (tpp80) REVERT: G 167 TRP cc_start: 0.5305 (m100) cc_final: 0.4756 (m100) outliers start: 85 outliers final: 52 residues processed: 608 average time/residue: 0.1975 time to fit residues: 192.4492 Evaluate side-chains 494 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 438 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 318 PHE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 595 VAL 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 935 GLN 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 604 THR 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 955 ASN 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 50 SER Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 325 SER 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 724 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 922 LEU 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 991 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 63 LYS 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 178 GLN 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 65 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 374 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 304 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 305 optimal weight: 0.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 536 ASN A 751 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 360 ASN B 644 GLN B 751 ASN B 856 ASN B 901 GLN B 925 ASN B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN B1088 HIS C 360 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1002 GLN C1159 HIS ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN E 142 ASN G 128 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.128269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.104321 restraints weight = 168331.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.104758 restraints weight = 103426.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.105187 restraints weight = 70131.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.105515 restraints weight = 60862.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.105600 restraints weight = 54225.458| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 32800 Z= 0.271 Angle : 0.770 15.229 44651 Z= 0.404 Chirality : 0.049 0.257 5019 Planarity : 0.005 0.060 5758 Dihedral : 5.177 33.477 4389 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.58 % Favored : 96.37 % Rotamer: Outliers : 3.60 % Allowed : 10.98 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.12), residues: 4048 helix: 0.36 (0.18), residues: 703 sheet: 0.06 (0.15), residues: 1082 loop : -1.01 (0.12), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B1039 TYR 0.025 0.003 TYR C 707 PHE 0.029 0.003 PHE C 855 TRP 0.020 0.002 TRP B 886 HIS 0.019 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00586 (32759) covalent geometry : angle 0.76828 (44569) SS BOND : bond 0.01495 ( 41) SS BOND : angle 1.54861 ( 82) hydrogen bonds : bond 0.04984 ( 1260) hydrogen bonds : angle 6.50613 ( 3528) *********************** 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 572 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 443 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1355 (ppp) cc_final: 0.0815 (pmm) REVERT: A 177 MET cc_start: 0.0585 (mmp) cc_final: 0.0356 (mmm) REVERT: A 287 ASP cc_start: 0.8810 (t0) cc_final: 0.8299 (m-30) REVERT: A 304 LYS cc_start: 0.9078 (mttt) cc_final: 0.8636 (tppt) REVERT: A 368 LEU cc_start: 0.3468 (mt) cc_final: 0.2842 (pt) REVERT: A 708 SER cc_start: 0.8556 (t) cc_final: 0.7880 (m) REVERT: A 786 LYS cc_start: 0.8949 (mmmt) cc_final: 0.8742 (mmmm) REVERT: A 988 GLU cc_start: 0.8746 (mp0) cc_final: 0.8520 (mp0) REVERT: A 996 LEU cc_start: 0.9531 (mp) cc_final: 0.9296 (mp) REVERT: A 1002 GLN cc_start: 0.9050 (mt0) cc_final: 0.8828 (tt0) REVERT: A 1017 GLU cc_start: 0.8569 (tp30) cc_final: 0.7992 (tm-30) REVERT: B 145 TYR cc_start: 0.3483 (p90) cc_final: 0.3187 (p90) REVERT: B 177 MET cc_start: 0.0536 (ttp) cc_final: -0.0614 (mmp) REVERT: B 695 TYR cc_start: 0.7324 (p90) cc_final: 0.6708 (p90) REVERT: B 765 ARG cc_start: 0.8743 (ptm160) cc_final: 0.8496 (ptp90) REVERT: B 928 ASN cc_start: 0.8824 (m-40) cc_final: 0.8518 (m-40) REVERT: B 1010 GLN cc_start: 0.8487 (tt0) cc_final: 0.8084 (tt0) REVERT: B 1014 ARG cc_start: 0.8677 (tpp80) cc_final: 0.8051 (tpp80) REVERT: B 1018 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8856 (mt) REVERT: B 1030 SER cc_start: 0.9391 (m) cc_final: 0.9175 (p) REVERT: C 54 LEU cc_start: 0.8394 (tp) cc_final: 0.8137 (tp) REVERT: C 564 GLN cc_start: 0.8771 (mt0) cc_final: 0.7969 (tp-100) REVERT: C 732 THR cc_start: 0.9394 (m) cc_final: 0.8993 (p) REVERT: C 765 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8175 (mtm110) REVERT: C 773 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8047 (mm-30) REVERT: C 859 THR cc_start: 0.8965 (m) cc_final: 0.8667 (p) REVERT: C 900 MET cc_start: 0.8501 (mmt) cc_final: 0.7128 (mmt) REVERT: C 955 ASN cc_start: 0.8489 (m110) cc_final: 0.7967 (m110) REVERT: C 965 GLN cc_start: 0.9076 (tp40) cc_final: 0.8400 (tp-100) REVERT: C 968 SER cc_start: 0.9423 (m) cc_final: 0.8860 (p) REVERT: C 991 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8667 (p) REVERT: C 995 ARG cc_start: 0.9231 (mtt180) cc_final: 0.8867 (mtm-85) REVERT: C 1002 GLN cc_start: 0.8986 (tt0) cc_final: 0.8740 (tm-30) REVERT: C 1014 ARG cc_start: 0.8903 (mmm-85) cc_final: 0.8650 (mmm-85) REVERT: C 1146 ASP cc_start: 0.8976 (t70) cc_final: 0.8670 (m-30) REVERT: F 46 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7947 (mp0) REVERT: F 64 PHE cc_start: 0.8574 (m-80) cc_final: 0.8274 (m-10) REVERT: F 81 MET cc_start: 0.6744 (ttp) cc_final: 0.5044 (ttp) REVERT: F 216 LYS cc_start: 0.6411 (mttt) cc_final: 0.6209 (mptt) REVERT: G 96 ARG cc_start: 0.7912 (tpt-90) cc_final: 0.7620 (tpp-160) REVERT: G 167 TRP cc_start: 0.5248 (m100) cc_final: 0.4724 (m100) outliers start: 129 outliers final: 85 residues processed: 526 average time/residue: 0.1849 time to fit residues: 159.2784 Evaluate side-chains 451 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 363 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 151 SER 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 323 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 595 VAL 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 763 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 976 VAL 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 A residue 1012 LEU 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 315 THR Chi-restraints excluded: chain B residue 318 PHE 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 604 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 737 ASP 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 821 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1121 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 294 ASP 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 494 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 777 ASN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1033 VAL 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 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 178 GLN 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 3 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 184 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 105 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 363 optimal weight: 20.0000 chunk 399 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 326 optimal weight: 0.0470 chunk 355 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 292 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 275 optimal weight: 5.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1010 GLN C 52 GLN C 644 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.127995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.105028 restraints weight = 168278.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.104816 restraints weight = 110969.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.105127 restraints weight = 78300.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.105285 restraints weight = 73939.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.105544 restraints weight = 61709.704| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 32800 Z= 0.178 Angle : 0.663 13.359 44651 Z= 0.342 Chirality : 0.046 0.274 5019 Planarity : 0.004 0.087 5758 Dihedral : 5.019 34.555 4389 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.18 % Rotamer: Outliers : 3.10 % Allowed : 12.46 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.12), residues: 4048 helix: 0.60 (0.18), residues: 704 sheet: 0.03 (0.15), residues: 1068 loop : -1.10 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 995 TYR 0.026 0.002 TYR D 103 PHE 0.024 0.002 PHE C1109 TRP 0.013 0.002 TRP A 886 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00401 (32759) covalent geometry : angle 0.66080 (44569) SS BOND : bond 0.00528 ( 41) SS BOND : angle 1.53167 ( 82) hydrogen bonds : bond 0.04245 ( 1260) hydrogen bonds : angle 6.10232 ( 3528) *********************** 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 522 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 411 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1438 (ppp) cc_final: 0.1077 (pmm) REVERT: A 177 MET cc_start: 0.0690 (mmp) cc_final: -0.0666 (mtp) REVERT: A 304 LYS cc_start: 0.9044 (mttt) cc_final: 0.8656 (tppt) REVERT: A 708 SER cc_start: 0.8517 (t) cc_final: 0.7925 (m) REVERT: A 758 SER cc_start: 0.8883 (p) cc_final: 0.8649 (t) REVERT: A 996 LEU cc_start: 0.9467 (mp) cc_final: 0.9167 (mp) REVERT: A 1002 GLN cc_start: 0.9008 (mt0) cc_final: 0.8785 (tt0) REVERT: A 1017 GLU cc_start: 0.8562 (tp30) cc_final: 0.7939 (tm-30) REVERT: A 1019 ARG cc_start: 0.8310 (tpt170) cc_final: 0.8028 (tpt170) REVERT: B 145 TYR cc_start: 0.3221 (p90) cc_final: 0.2950 (p90) REVERT: B 177 MET cc_start: 0.0384 (ttp) cc_final: -0.0786 (mmt) REVERT: B 695 TYR cc_start: 0.7470 (p90) cc_final: 0.6400 (p90) REVERT: B 756 TYR cc_start: 0.9293 (m-80) cc_final: 0.9004 (m-80) REVERT: B 902 MET cc_start: 0.9091 (tpp) cc_final: 0.8845 (tpp) REVERT: B 928 ASN cc_start: 0.8793 (m-40) cc_final: 0.8488 (m-40) REVERT: B 995 ARG cc_start: 0.8837 (mtm-85) cc_final: 0.8520 (mtm-85) REVERT: B 1014 ARG cc_start: 0.8691 (tpp80) cc_final: 0.8308 (tpp80) REVERT: B 1023 ASN cc_start: 0.9007 (m-40) cc_final: 0.8713 (m110) REVERT: B 1030 SER cc_start: 0.9511 (m) cc_final: 0.9202 (p) REVERT: C 54 LEU cc_start: 0.8548 (tp) cc_final: 0.8265 (tp) REVERT: C 177 MET cc_start: 0.1299 (mtp) cc_final: 0.0634 (mtm) REVERT: C 564 GLN cc_start: 0.8673 (mt0) cc_final: 0.8213 (tp-100) REVERT: C 732 THR cc_start: 0.9423 (m) cc_final: 0.9177 (p) REVERT: C 765 ARG cc_start: 0.8456 (mtm110) cc_final: 0.8174 (mtm-85) REVERT: C 773 GLU cc_start: 0.8231 (mm-30) cc_final: 0.8024 (mm-30) REVERT: C 859 THR cc_start: 0.8968 (m) cc_final: 0.8694 (p) REVERT: C 902 MET cc_start: 0.9112 (tpp) cc_final: 0.8897 (tpp) REVERT: C 955 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8020 (m110) REVERT: C 965 GLN cc_start: 0.8861 (tp40) cc_final: 0.8307 (tp40) REVERT: C 968 SER cc_start: 0.9339 (m) cc_final: 0.8942 (p) REVERT: C 978 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.7991 (p0) REVERT: C 995 ARG cc_start: 0.9149 (mtt180) cc_final: 0.8889 (mtm-85) REVERT: C 1014 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8468 (mmm-85) REVERT: F 46 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7691 (pm20) REVERT: F 98 ARG cc_start: 0.5987 (mmm160) cc_final: 0.5502 (mmm160) REVERT: G 96 ARG cc_start: 0.8094 (tpt-90) cc_final: 0.7877 (tpp-160) outliers start: 111 outliers final: 76 residues processed: 484 average time/residue: 0.1887 time to fit residues: 149.3551 Evaluate side-chains 448 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 370 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 192 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE 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 617 CYS Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 739 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 959 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 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1012 LEU 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 318 PHE Chi-restraints excluded: chain B residue 452 LEU 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 736 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 860 VAL 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 1121 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 148 ASN 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 401 VAL Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 955 ASN 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 50 MET 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 21 ILE 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 107 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 244 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 308 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 204 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 644 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.127973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.104279 restraints weight = 167973.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.104938 restraints weight = 105286.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.105479 restraints weight = 71404.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.105769 restraints weight = 58895.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.106018 restraints weight = 52404.811| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 32800 Z= 0.143 Angle : 0.631 10.776 44651 Z= 0.320 Chirality : 0.045 0.334 5019 Planarity : 0.004 0.059 5758 Dihedral : 4.837 33.308 4389 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.59 % Rotamer: Outliers : 2.60 % Allowed : 14.05 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.12), residues: 4048 helix: 0.84 (0.19), residues: 699 sheet: 0.10 (0.15), residues: 1096 loop : -1.08 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1014 TYR 0.022 0.001 TYR A1138 PHE 0.026 0.002 PHE C 306 TRP 0.018 0.001 TRP B 886 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00327 (32759) covalent geometry : angle 0.62845 (44569) SS BOND : bond 0.00363 ( 41) SS BOND : angle 1.35274 ( 82) hydrogen bonds : bond 0.03951 ( 1260) hydrogen bonds : angle 5.88202 ( 3528) *********************** 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 501 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 408 time to evaluate : 1.194 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: A 153 MET cc_start: 0.1278 (ppp) cc_final: 0.0961 (pmm) REVERT: A 177 MET cc_start: 0.0935 (mmp) cc_final: -0.0388 (mtp) REVERT: A 304 LYS cc_start: 0.8976 (mttt) cc_final: 0.8624 (tppt) REVERT: A 708 SER cc_start: 0.8450 (t) cc_final: 0.7864 (m) REVERT: A 817 PHE cc_start: 0.8202 (t80) cc_final: 0.7917 (t80) REVERT: A 1002 GLN cc_start: 0.9017 (mt0) cc_final: 0.8801 (tt0) REVERT: A 1017 GLU cc_start: 0.8464 (tp30) cc_final: 0.7856 (tm-30) REVERT: A 1019 ARG cc_start: 0.8232 (tpt170) cc_final: 0.7937 (tpt-90) REVERT: A 1052 PHE cc_start: 0.7991 (m-10) cc_final: 0.7772 (m-80) REVERT: B 177 MET cc_start: 0.0558 (ttp) cc_final: -0.0718 (mmt) REVERT: B 278 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7030 (mptt) REVERT: B 695 TYR cc_start: 0.7528 (p90) cc_final: 0.6284 (p90) REVERT: B 756 TYR cc_start: 0.9193 (m-80) cc_final: 0.8951 (m-80) REVERT: B 765 ARG cc_start: 0.8468 (ptp90) cc_final: 0.8000 (ptp90) REVERT: B 900 MET cc_start: 0.7995 (mtt) cc_final: 0.7775 (mtt) REVERT: B 928 ASN cc_start: 0.8717 (m-40) cc_final: 0.8381 (m-40) REVERT: B 995 ARG cc_start: 0.8797 (mtm-85) cc_final: 0.8352 (mtm-85) REVERT: B 1010 GLN cc_start: 0.8279 (tt0) cc_final: 0.7446 (tt0) REVERT: B 1014 ARG cc_start: 0.8576 (tpp80) cc_final: 0.8092 (tpp80) REVERT: B 1023 ASN cc_start: 0.8906 (m-40) cc_final: 0.8242 (m110) REVERT: C 54 LEU cc_start: 0.8545 (tp) cc_final: 0.8238 (tp) REVERT: C 153 MET cc_start: 0.7518 (mmt) cc_final: 0.7293 (mmm) REVERT: C 177 MET cc_start: 0.1462 (mtp) cc_final: 0.0704 (mtm) REVERT: C 564 GLN cc_start: 0.8794 (mt0) cc_final: 0.7828 (tp-100) REVERT: C 732 THR cc_start: 0.9421 (m) cc_final: 0.9156 (p) REVERT: C 762 GLN cc_start: 0.8079 (mm110) cc_final: 0.7747 (mm110) REVERT: C 765 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8143 (mtm-85) REVERT: C 859 THR cc_start: 0.8947 (m) cc_final: 0.8659 (p) REVERT: C 900 MET cc_start: 0.8373 (mmt) cc_final: 0.8124 (mmt) REVERT: C 902 MET cc_start: 0.9069 (tpp) cc_final: 0.8867 (tpp) REVERT: C 955 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.7921 (m110) REVERT: C 965 GLN cc_start: 0.8722 (tp40) cc_final: 0.8259 (tp40) REVERT: C 968 SER cc_start: 0.9324 (m) cc_final: 0.9015 (p) REVERT: C 995 ARG cc_start: 0.9095 (mtt180) cc_final: 0.8789 (mtm-85) REVERT: C 1002 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8409 (tm-30) REVERT: C 1014 ARG cc_start: 0.8614 (mmm-85) cc_final: 0.8351 (mmm-85) REVERT: F 46 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7734 (pm20) outliers start: 93 outliers final: 66 residues processed: 467 average time/residue: 0.1840 time to fit residues: 141.4469 Evaluate side-chains 434 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 365 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 192 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU 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 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 278 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 318 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 604 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 860 VAL 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 980 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain D residue 50 MET 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 21 ILE 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 G residue 41 GLN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 107 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 366 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 289 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 313 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 532 ASN B 856 ASN B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN B1101 HIS C 321 GLN C 487 ASN C 751 ASN C 913 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.123148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.100505 restraints weight = 169811.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.100690 restraints weight = 116505.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.100976 restraints weight = 79454.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.101172 restraints weight = 68634.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.101388 restraints weight = 64707.135| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.7248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 32800 Z= 0.262 Angle : 0.762 13.320 44651 Z= 0.395 Chirality : 0.048 0.273 5019 Planarity : 0.005 0.083 5758 Dihedral : 5.523 37.541 4389 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.77 % Favored : 95.18 % Rotamer: Outliers : 3.32 % Allowed : 14.78 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.12), residues: 4048 helix: 0.48 (0.19), residues: 713 sheet: -0.06 (0.15), residues: 1085 loop : -1.37 (0.12), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 995 TYR 0.022 0.002 TYR D 109 PHE 0.029 0.002 PHE A 927 TRP 0.019 0.002 TRP A 64 HIS 0.012 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00582 (32759) covalent geometry : angle 0.75797 (44569) SS BOND : bond 0.00659 ( 41) SS BOND : angle 1.92509 ( 82) hydrogen bonds : bond 0.04601 ( 1260) hydrogen bonds : angle 6.40370 ( 3528) *********************** 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 502 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 383 time to evaluate : 0.935 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 23 GLN cc_start: 0.6352 (tt0) cc_final: 0.5862 (mp10) REVERT: A 177 MET cc_start: 0.1601 (mmp) cc_final: 0.0058 (mtp) REVERT: A 1002 GLN cc_start: 0.9023 (mt0) cc_final: 0.8800 (tt0) REVERT: A 1017 GLU cc_start: 0.8540 (tp30) cc_final: 0.7967 (tm-30) REVERT: A 1019 ARG cc_start: 0.8262 (tpt170) cc_final: 0.8004 (tpt170) REVERT: B 128 ILE cc_start: 0.9118 (mm) cc_final: 0.8900 (mm) REVERT: B 145 TYR cc_start: 0.3595 (p90) cc_final: 0.3306 (p90) REVERT: B 177 MET cc_start: 0.0415 (ttp) cc_final: -0.0869 (mmt) REVERT: B 278 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.6624 (mptt) REVERT: B 765 ARG cc_start: 0.8653 (ptp90) cc_final: 0.8167 (ptp90) REVERT: B 928 ASN cc_start: 0.8897 (m-40) cc_final: 0.8605 (m-40) REVERT: B 995 ARG cc_start: 0.8819 (mtm-85) cc_final: 0.8510 (mtm-85) REVERT: B 1010 GLN cc_start: 0.8231 (tt0) cc_final: 0.7409 (tt0) REVERT: B 1014 ARG cc_start: 0.8688 (tpp80) cc_final: 0.8182 (tpp80) REVERT: B 1019 ARG cc_start: 0.8844 (mmm160) cc_final: 0.8242 (tpt170) REVERT: B 1023 ASN cc_start: 0.8903 (m110) cc_final: 0.8673 (m-40) REVERT: B 1029 MET cc_start: 0.8654 (tpp) cc_final: 0.8297 (tpp) REVERT: C 50 SER cc_start: 0.9410 (m) cc_final: 0.9100 (p) REVERT: C 54 LEU cc_start: 0.8693 (tp) cc_final: 0.8338 (tp) REVERT: C 177 MET cc_start: 0.2480 (mtp) cc_final: 0.1205 (mtm) REVERT: C 195 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8229 (ptmm) REVERT: C 731 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8691 (ttp) REVERT: C 732 THR cc_start: 0.9447 (m) cc_final: 0.9216 (p) REVERT: C 755 GLN cc_start: 0.8930 (mt0) cc_final: 0.8604 (mt0) REVERT: C 762 GLN cc_start: 0.8254 (mm110) cc_final: 0.7917 (mm110) REVERT: C 765 ARG cc_start: 0.8292 (mtm110) cc_final: 0.8087 (mtm-85) REVERT: C 790 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8650 (mtpt) REVERT: C 859 THR cc_start: 0.8934 (m) cc_final: 0.8667 (p) REVERT: C 864 LEU cc_start: 0.8370 (tt) cc_final: 0.7736 (mm) REVERT: C 904 TYR cc_start: 0.7148 (t80) cc_final: 0.6562 (t80) REVERT: C 965 GLN cc_start: 0.8701 (tp40) cc_final: 0.8406 (tp40) REVERT: C 978 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8138 (p0) REVERT: C 1002 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8431 (tm-30) REVERT: C 1005 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7773 (tm-30) REVERT: C 1014 ARG cc_start: 0.8666 (mmm-85) cc_final: 0.8464 (mmm-85) REVERT: C 1028 LYS cc_start: 0.9243 (mmtp) cc_final: 0.8939 (mmtm) REVERT: C 1031 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7883 (mt-10) REVERT: C 1115 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9018 (mp) REVERT: F 81 MET cc_start: 0.6160 (tpp) cc_final: 0.5691 (tpp) REVERT: F 89 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7316 (tm-30) REVERT: F 155 GLU cc_start: 0.6347 (mm-30) cc_final: 0.6144 (mm-30) REVERT: G 90 TYR cc_start: 0.7378 (m-80) cc_final: 0.6997 (m-80) outliers start: 119 outliers final: 94 residues processed: 466 average time/residue: 0.1890 time to fit residues: 144.2215 Evaluate side-chains 442 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 343 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 192 PHE 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 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 617 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 767 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 916 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 964 LYS 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 B residue 173 GLN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 278 LYS 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 324 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU 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 736 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 934 ILE 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 996 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 534 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 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 959 LEU 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 1077 THR Chi-restraints excluded: chain C residue 1115 ILE 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 70 LEU 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 57 GLU 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 Chi-restraints excluded: chain G residue 41 GLN Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 151 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 171 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 380 optimal weight: 6.9990 chunk 232 optimal weight: 8.9990 chunk 307 optimal weight: 0.9990 chunk 330 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 856 ASN B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.123056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.100042 restraints weight = 169265.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.100838 restraints weight = 112616.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.101121 restraints weight = 70773.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.101364 restraints weight = 65795.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.101524 restraints weight = 59369.595| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.7620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 32800 Z= 0.215 Angle : 0.723 13.469 44651 Z= 0.369 Chirality : 0.047 0.305 5019 Planarity : 0.005 0.059 5758 Dihedral : 5.434 38.027 4389 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.57 % Favored : 95.38 % Rotamer: Outliers : 3.60 % Allowed : 15.03 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.12), residues: 4048 helix: 0.56 (0.19), residues: 715 sheet: -0.08 (0.15), residues: 1080 loop : -1.44 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1014 TYR 0.045 0.002 TYR D 103 PHE 0.035 0.002 PHE A 497 TRP 0.017 0.002 TRP A 64 HIS 0.007 0.001 HIS E 94 Details of bonding type rmsd covalent geometry : bond 0.00486 (32759) covalent geometry : angle 0.72046 (44569) SS BOND : bond 0.00401 ( 41) SS BOND : angle 1.70311 ( 82) hydrogen bonds : bond 0.04255 ( 1260) hydrogen bonds : angle 6.29858 ( 3528) *********************** 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 501 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 372 time to evaluate : 1.178 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 23 GLN cc_start: 0.6310 (tt0) cc_final: 0.5755 (mp10) REVERT: A 177 MET cc_start: 0.1828 (mmp) cc_final: 0.0283 (mtp) REVERT: A 303 LEU cc_start: 0.9534 (tp) cc_final: 0.9230 (tt) REVERT: A 1017 GLU cc_start: 0.8483 (tp30) cc_final: 0.8015 (tm-30) REVERT: B 145 TYR cc_start: 0.3613 (p90) cc_final: 0.3375 (p90) REVERT: B 176 LEU cc_start: -0.2073 (OUTLIER) cc_final: -0.2613 (pp) REVERT: B 177 MET cc_start: 0.1021 (ttp) cc_final: -0.0293 (mpp) REVERT: B 195 LYS cc_start: 0.8171 (ptmt) cc_final: 0.7525 (pttm) REVERT: B 278 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.6362 (mptt) REVERT: B 380 TYR cc_start: 0.3971 (OUTLIER) cc_final: 0.3466 (m-10) REVERT: B 765 ARG cc_start: 0.8658 (ptp90) cc_final: 0.8134 (ptp90) REVERT: B 900 MET cc_start: 0.8377 (mtt) cc_final: 0.8149 (mtt) REVERT: B 928 ASN cc_start: 0.8853 (m-40) cc_final: 0.8544 (m-40) REVERT: B 983 ARG cc_start: 0.7685 (mtm180) cc_final: 0.7454 (tpm170) REVERT: B 995 ARG cc_start: 0.8796 (mtm-85) cc_final: 0.8486 (mtm-85) REVERT: B 1014 ARG cc_start: 0.8630 (tpp80) cc_final: 0.8248 (tpp80) REVERT: B 1019 ARG cc_start: 0.8794 (mmm160) cc_final: 0.8253 (tpt170) REVERT: C 50 SER cc_start: 0.9380 (m) cc_final: 0.9117 (p) REVERT: C 54 LEU cc_start: 0.8786 (tp) cc_final: 0.8498 (tp) REVERT: C 177 MET cc_start: 0.2867 (mtp) cc_final: 0.1542 (mtm) REVERT: C 195 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8278 (ptmm) REVERT: C 732 THR cc_start: 0.9408 (m) cc_final: 0.9081 (p) REVERT: C 755 GLN cc_start: 0.8970 (mt0) cc_final: 0.8731 (mt0) REVERT: C 762 GLN cc_start: 0.8254 (mm110) cc_final: 0.8030 (mm110) REVERT: C 765 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8072 (mtm-85) REVERT: C 790 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8627 (mtpt) REVERT: C 859 THR cc_start: 0.8909 (m) cc_final: 0.8633 (p) REVERT: C 902 MET cc_start: 0.9091 (tpp) cc_final: 0.8586 (mmp) REVERT: C 1002 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8624 (tm-30) REVERT: C 1005 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7767 (tm-30) REVERT: C 1028 LYS cc_start: 0.9100 (mmtp) cc_final: 0.8578 (mmtm) REVERT: C 1115 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8989 (mp) REVERT: D 46 GLU cc_start: 0.8244 (pm20) cc_final: 0.7880 (mm-30) REVERT: F 81 MET cc_start: 0.6120 (tpp) cc_final: 0.5646 (tpp) REVERT: F 98 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.6247 (mmm160) REVERT: F 155 GLU cc_start: 0.6016 (mm-30) cc_final: 0.5792 (mm-30) outliers start: 129 outliers final: 92 residues processed: 468 average time/residue: 0.1954 time to fit residues: 149.4407 Evaluate side-chains 433 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 334 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 276 LEU 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 572 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 767 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 916 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 966 LEU 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 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 92 PHE 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 278 LYS 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 324 GLU 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 604 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 934 ILE 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 981 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1115 ILE 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 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 71 THR Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain F residue 107 PHE Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 151 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 352 optimal weight: 7.9990 chunk 267 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 304 optimal weight: 8.9990 chunk 264 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 218 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN B 856 ASN B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 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 = 0.4315 r_free = 0.4315 target = 0.122786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.096366 restraints weight = 157469.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.098340 restraints weight = 85418.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.099565 restraints weight = 55010.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.100524 restraints weight = 40558.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.101028 restraints weight = 32923.193| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.7802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 32800 Z= 0.161 Angle : 0.695 13.205 44651 Z= 0.350 Chirality : 0.047 0.289 5019 Planarity : 0.004 0.071 5758 Dihedral : 5.209 36.066 4389 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.40 % Favored : 95.55 % Rotamer: Outliers : 2.99 % Allowed : 16.15 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.13), residues: 4048 helix: 0.68 (0.19), residues: 714 sheet: -0.04 (0.15), residues: 1074 loop : -1.36 (0.12), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1014 TYR 0.033 0.002 TYR F 101 PHE 0.047 0.002 PHE B 562 TRP 0.019 0.002 TRP D 106 HIS 0.005 0.001 HIS E 94 Details of bonding type rmsd covalent geometry : bond 0.00367 (32759) covalent geometry : angle 0.69253 (44569) SS BOND : bond 0.00459 ( 41) SS BOND : angle 1.60944 ( 82) hydrogen bonds : bond 0.04005 ( 1260) hydrogen bonds : angle 6.11779 ( 3528) *********************** 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 477 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 370 time to evaluate : 0.955 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: A 23 GLN cc_start: 0.5971 (tt0) cc_final: 0.5644 (mp10) REVERT: A 177 MET cc_start: 0.1739 (mmp) cc_final: 0.0234 (mtp) REVERT: A 276 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8198 (tp) REVERT: A 287 ASP cc_start: 0.8591 (t70) cc_final: 0.7794 (m-30) REVERT: A 303 LEU cc_start: 0.9471 (tp) cc_final: 0.9200 (tt) REVERT: A 699 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8315 (mt) REVERT: A 708 SER cc_start: 0.8396 (t) cc_final: 0.7872 (m) REVERT: A 992 GLN cc_start: 0.8578 (mm110) cc_final: 0.8352 (mm110) REVERT: A 1017 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: B 177 MET cc_start: -0.0032 (ttp) cc_final: -0.0953 (mpp) REVERT: B 195 LYS cc_start: 0.8097 (ptmt) cc_final: 0.7418 (pttm) REVERT: B 380 TYR cc_start: 0.3900 (OUTLIER) cc_final: 0.3344 (m-10) REVERT: B 765 ARG cc_start: 0.8594 (ptp90) cc_final: 0.8081 (ptp90) REVERT: B 928 ASN cc_start: 0.8732 (m-40) cc_final: 0.8457 (m-40) REVERT: B 995 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8465 (ttp-170) REVERT: B 1010 GLN cc_start: 0.8185 (tt0) cc_final: 0.7171 (tt0) REVERT: B 1014 ARG cc_start: 0.8535 (tpp80) cc_final: 0.8117 (tpp80) REVERT: C 50 SER cc_start: 0.9337 (m) cc_final: 0.9054 (p) REVERT: C 54 LEU cc_start: 0.8764 (tp) cc_final: 0.8477 (tp) REVERT: C 177 MET cc_start: 0.2621 (mtp) cc_final: 0.1574 (mtm) REVERT: C 195 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8266 (ptmm) REVERT: C 732 THR cc_start: 0.9426 (m) cc_final: 0.9119 (p) REVERT: C 755 GLN cc_start: 0.8831 (mt0) cc_final: 0.8376 (tt0) REVERT: C 764 ASN cc_start: 0.8420 (m-40) cc_final: 0.8201 (m110) REVERT: C 765 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7944 (mtm110) REVERT: C 790 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8622 (mtpt) REVERT: C 859 THR cc_start: 0.8889 (m) cc_final: 0.8630 (p) REVERT: C 902 MET cc_start: 0.9122 (tpp) cc_final: 0.8610 (mmp) REVERT: C 955 ASN cc_start: 0.8689 (m110) cc_final: 0.8054 (m-40) REVERT: C 965 GLN cc_start: 0.8504 (tp40) cc_final: 0.8117 (tp-100) REVERT: C 1002 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8811 (tm-30) REVERT: C 1005 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7902 (tm-30) REVERT: C 1115 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8889 (mp) REVERT: D 34 MET cc_start: 0.6838 (tpp) cc_final: 0.6462 (tpp) REVERT: D 46 GLU cc_start: 0.7860 (pm20) cc_final: 0.7551 (pm20) REVERT: F 81 MET cc_start: 0.5888 (tpp) cc_final: 0.5460 (tpp) REVERT: G 90 TYR cc_start: 0.7182 (m-80) cc_final: 0.6615 (m-80) outliers start: 107 outliers final: 78 residues processed: 445 average time/residue: 0.1884 time to fit residues: 136.4211 Evaluate side-chains 434 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 349 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 151 SER Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE 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 699 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 767 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 916 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 324 GLU 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 604 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1115 ILE 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 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 Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 151 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 113 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 378 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 377 optimal weight: 9.9990 chunk 354 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 345 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 271 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 474 GLN B 564 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN C 314 GLN C 564 GLN C 913 GLN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN F 178 GLN G 41 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.115975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.090873 restraints weight = 158448.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.092797 restraints weight = 91175.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.093268 restraints weight = 63508.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.094332 restraints weight = 46304.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.094463 restraints weight = 35417.520| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.8517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 32800 Z= 0.274 Angle : 0.824 12.889 44651 Z= 0.423 Chirality : 0.050 0.365 5019 Planarity : 0.006 0.070 5758 Dihedral : 5.905 40.439 4389 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.57 % Favored : 93.40 % Rotamer: Outliers : 3.18 % Allowed : 16.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.12), residues: 4048 helix: 0.13 (0.18), residues: 726 sheet: -0.31 (0.15), residues: 1100 loop : -1.57 (0.12), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 983 TYR 0.045 0.003 TYR F 101 PHE 0.033 0.003 PHE A 497 TRP 0.026 0.003 TRP D 33 HIS 0.008 0.002 HIS E 94 Details of bonding type rmsd covalent geometry : bond 0.00618 (32759) covalent geometry : angle 0.81962 (44569) SS BOND : bond 0.00608 ( 41) SS BOND : angle 2.09076 ( 82) hydrogen bonds : bond 0.04744 ( 1260) hydrogen bonds : angle 6.67598 ( 3528) *********************** 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 463 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 349 time to evaluate : 1.010 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 23 GLN cc_start: 0.6638 (tt0) cc_final: 0.5765 (mp10) REVERT: A 177 MET cc_start: 0.1696 (mmp) cc_final: 0.0510 (mtp) REVERT: A 276 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8119 (tp) REVERT: A 287 ASP cc_start: 0.8762 (t70) cc_final: 0.7995 (m-30) REVERT: A 303 LEU cc_start: 0.9446 (tp) cc_final: 0.9133 (tt) REVERT: A 730 SER cc_start: 0.9280 (OUTLIER) cc_final: 0.9079 (m) REVERT: A 1001 LEU cc_start: 0.9512 (tp) cc_final: 0.9300 (tt) REVERT: A 1005 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8546 (mm110) REVERT: A 1017 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: B 145 TYR cc_start: 0.3620 (p90) cc_final: 0.3338 (p90) REVERT: B 176 LEU cc_start: -0.2020 (OUTLIER) cc_final: -0.2461 (pp) REVERT: B 177 MET cc_start: -0.0367 (ttp) cc_final: -0.1079 (mpp) REVERT: B 195 LYS cc_start: 0.8217 (ptmt) cc_final: 0.7544 (pttm) REVERT: B 336 CYS cc_start: 0.2109 (OUTLIER) cc_final: 0.0202 (t) REVERT: B 380 TYR cc_start: 0.3823 (OUTLIER) cc_final: 0.3430 (m-10) REVERT: B 765 ARG cc_start: 0.8695 (ptp90) cc_final: 0.8142 (ptp90) REVERT: B 928 ASN cc_start: 0.8887 (m-40) cc_final: 0.8635 (m-40) REVERT: B 995 ARG cc_start: 0.8771 (mtm-85) cc_final: 0.8423 (mtm-85) REVERT: B 1014 ARG cc_start: 0.8638 (tpp80) cc_final: 0.8196 (tpp80) REVERT: C 54 LEU cc_start: 0.8916 (tp) cc_final: 0.8677 (tp) REVERT: C 153 MET cc_start: 0.6910 (mmm) cc_final: 0.6594 (mmm) REVERT: C 177 MET cc_start: 0.2961 (mtp) cc_final: 0.1787 (mtm) REVERT: C 195 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8258 (ptmm) REVERT: C 298 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8211 (mm-30) REVERT: C 543 PHE cc_start: 0.7419 (m-80) cc_final: 0.7116 (m-80) REVERT: C 732 THR cc_start: 0.9503 (m) cc_final: 0.9292 (p) REVERT: C 755 GLN cc_start: 0.8974 (mt0) cc_final: 0.8675 (tt0) REVERT: C 790 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8672 (mtpt) REVERT: C 859 THR cc_start: 0.8889 (m) cc_final: 0.8648 (p) REVERT: C 911 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8824 (p) REVERT: C 957 GLN cc_start: 0.8580 (tp-100) cc_final: 0.8304 (tp-100) REVERT: C 978 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8314 (p0) REVERT: C 1002 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8614 (tm-30) REVERT: D 46 GLU cc_start: 0.7859 (pm20) cc_final: 0.7518 (pm20) REVERT: F 11 LEU cc_start: 0.4763 (tp) cc_final: 0.4546 (tp) REVERT: F 71 THR cc_start: 0.7959 (OUTLIER) cc_final: 0.7716 (p) REVERT: F 81 MET cc_start: 0.6022 (tpp) cc_final: 0.5609 (tpp) REVERT: F 98 ARG cc_start: 0.6128 (OUTLIER) cc_final: 0.5460 (mmm160) REVERT: F 99 LYS cc_start: 0.8856 (tttt) cc_final: 0.8427 (pttm) REVERT: G 90 TYR cc_start: 0.7640 (m-80) cc_final: 0.7137 (m-80) REVERT: G 127 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6881 (tm-30) outliers start: 114 outliers final: 83 residues processed: 433 average time/residue: 0.1881 time to fit residues: 133.7717 Evaluate side-chains 425 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 330 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE 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 729 VAL Chi-restraints excluded: chain A residue 730 SER 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 916 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 62 VAL 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 305 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 336 CYS 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 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 750 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 860 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 620 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 716 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 911 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 959 LEU 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 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 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 140 ASN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 127 GLU 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 178 optimal weight: 0.9990 chunk 320 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 333 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 267 optimal weight: 6.9990 chunk 240 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 856 ASN B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.117082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.091560 restraints weight = 160345.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.093328 restraints weight = 87969.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.094393 restraints weight = 56996.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.095161 restraints weight = 42354.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.095675 restraints weight = 34796.291| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.8561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.383 32800 Z= 0.280 Angle : 0.956 59.200 44651 Z= 0.499 Chirality : 0.049 0.292 5019 Planarity : 0.006 0.067 5758 Dihedral : 5.903 40.423 4389 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 24.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.57 % Favored : 93.40 % Rotamer: Outliers : 2.88 % Allowed : 17.09 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.12), residues: 4048 helix: 0.12 (0.18), residues: 720 sheet: -0.37 (0.15), residues: 1086 loop : -1.59 (0.12), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 765 TYR 0.044 0.002 TYR F 101 PHE 0.032 0.002 PHE A 497 TRP 0.022 0.003 TRP D 33 HIS 0.008 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00677 (32759) covalent geometry : angle 0.91441 (44569) SS BOND : bond 0.03052 ( 41) SS BOND : angle 6.57554 ( 82) hydrogen bonds : bond 0.04685 ( 1260) hydrogen bonds : angle 6.66813 ( 3528) ********************** 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 440 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 337 time to evaluate : 1.218 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: A 23 GLN cc_start: 0.6498 (tt0) cc_final: 0.5712 (mp10) REVERT: A 168 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6004 (m-80) REVERT: A 177 MET cc_start: 0.1787 (mmp) cc_final: 0.0584 (mtp) REVERT: A 276 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8105 (tp) REVERT: A 287 ASP cc_start: 0.8740 (t70) cc_final: 0.7977 (m-30) REVERT: A 303 LEU cc_start: 0.9463 (tp) cc_final: 0.9141 (tt) REVERT: A 730 SER cc_start: 0.9280 (OUTLIER) cc_final: 0.9074 (m) REVERT: A 1001 LEU cc_start: 0.9515 (tp) cc_final: 0.9307 (tt) REVERT: A 1005 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8570 (mm110) REVERT: A 1017 GLU cc_start: 0.8565 (tp30) cc_final: 0.7946 (tm-30) REVERT: B 145 TYR cc_start: 0.3473 (p90) cc_final: 0.3178 (p90) REVERT: B 176 LEU cc_start: -0.2124 (OUTLIER) cc_final: -0.2585 (pp) REVERT: B 177 MET cc_start: -0.0757 (ttp) cc_final: -0.1329 (mpp) REVERT: B 195 LYS cc_start: 0.8200 (ptmt) cc_final: 0.7542 (pttm) REVERT: B 336 CYS cc_start: 0.2066 (OUTLIER) cc_final: 0.0158 (t) REVERT: B 380 TYR cc_start: 0.3752 (OUTLIER) cc_final: 0.3378 (m-10) REVERT: B 765 ARG cc_start: 0.8628 (ptp90) cc_final: 0.8099 (ptp90) REVERT: B 995 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8375 (mtm-85) REVERT: B 1014 ARG cc_start: 0.8595 (tpp80) cc_final: 0.8216 (tpp80) REVERT: C 54 LEU cc_start: 0.8919 (tp) cc_final: 0.8679 (tp) REVERT: C 153 MET cc_start: 0.6674 (mmm) cc_final: 0.6361 (mmm) REVERT: C 177 MET cc_start: 0.2904 (mtp) cc_final: 0.1749 (mtm) REVERT: C 195 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8250 (ptmm) REVERT: C 298 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8196 (mm-30) REVERT: C 543 PHE cc_start: 0.7350 (m-80) cc_final: 0.7088 (m-80) REVERT: C 755 GLN cc_start: 0.8951 (mt0) cc_final: 0.8667 (tt0) REVERT: C 790 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8662 (mtpt) REVERT: C 859 THR cc_start: 0.8885 (m) cc_final: 0.8654 (p) REVERT: C 911 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8800 (p) REVERT: C 955 ASN cc_start: 0.8773 (m110) cc_final: 0.8306 (m-40) REVERT: C 957 GLN cc_start: 0.8502 (tp-100) cc_final: 0.8235 (tp-100) REVERT: C 978 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8292 (p0) REVERT: C 1002 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8610 (tm-30) REVERT: D 46 GLU cc_start: 0.7801 (pm20) cc_final: 0.7471 (pm20) REVERT: F 71 THR cc_start: 0.7917 (OUTLIER) cc_final: 0.7689 (p) REVERT: F 81 MET cc_start: 0.5901 (tpp) cc_final: 0.5514 (tpp) REVERT: F 98 ARG cc_start: 0.5987 (OUTLIER) cc_final: 0.5293 (mmm160) REVERT: F 99 LYS cc_start: 0.8861 (tttt) cc_final: 0.8418 (pttm) REVERT: G 90 TYR cc_start: 0.7460 (m-80) cc_final: 0.6947 (m-80) outliers start: 103 outliers final: 86 residues processed: 415 average time/residue: 0.1857 time to fit residues: 127.3409 Evaluate side-chains 425 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 328 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR 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 276 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 358 ILE 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 729 VAL Chi-restraints excluded: chain A residue 730 SER 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 916 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 966 LEU 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 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 62 VAL 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 305 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 336 CYS 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 531 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 750 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 860 VAL Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 620 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 716 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 911 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 968 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 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 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 G residue 5 THR Chi-restraints excluded: chain G residue 107 LYS 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 203 optimal weight: 3.9990 chunk 225 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 377 optimal weight: 50.0000 chunk 249 optimal weight: 0.7980 chunk 318 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A1054 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN C1058 HIS D 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.117790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.092576 restraints weight = 158201.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.095141 restraints weight = 88420.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.095532 restraints weight = 50556.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.096039 restraints weight = 36416.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.096063 restraints weight = 37754.180| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.8547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 32800 Z= 0.183 Angle : 0.771 19.780 44651 Z= 0.389 Chirality : 0.048 0.313 5019 Planarity : 0.005 0.083 5758 Dihedral : 5.670 38.789 4389 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.66 % Rotamer: Outliers : 2.54 % Allowed : 17.51 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.12), residues: 4048 helix: 0.26 (0.19), residues: 722 sheet: -0.30 (0.15), residues: 1083 loop : -1.52 (0.12), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 765 TYR 0.023 0.002 TYR B1007 PHE 0.031 0.002 PHE A 497 TRP 0.017 0.002 TRP D 33 HIS 0.007 0.001 HIS E 94 Details of bonding type rmsd covalent geometry : bond 0.00417 (32759) covalent geometry : angle 0.76489 (44569) SS BOND : bond 0.00749 ( 41) SS BOND : angle 2.32085 ( 82) hydrogen bonds : bond 0.04282 ( 1260) hydrogen bonds : angle 6.49243 ( 3528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6706.03 seconds wall clock time: 116 minutes 18.79 seconds (6978.79 seconds total)