Starting phenix.real_space_refine on Fri Jun 27 09:27:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wdf_32437/06_2025/7wdf_32437.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wdf_32437/06_2025/7wdf_32437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wdf_32437/06_2025/7wdf_32437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wdf_32437/06_2025/7wdf_32437.map" model { file = "/net/cci-nas-00/data/ceres_data/7wdf_32437/06_2025/7wdf_32437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wdf_32437/06_2025/7wdf_32437.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.124 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 145 5.16 5 C 20377 2.51 5 N 5342 2.21 5 O 6134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31998 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 2, 'PTRANS': 52, 'TRANS': 1024} Chain breaks: 8 Chain: "B" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1025} Chain breaks: 8 Chain: "C" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1025} Chain breaks: 8 Chain: "D" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "E" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Chain: "F" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "G" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 16.60, per 1000 atoms: 0.52 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: 7.28 Conformation dependent library (CDL) restraints added in 4.1 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: 5.32 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: 15.34 Time building geometry restraints manager: 8.78 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: 0.02 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.340 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 72.840 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.890 ------------------------------------------------------------------------------- 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 : 7.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.27 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.11), residues: 4048 helix: -2.52 (0.13), residues: 663 sheet: -0.30 (0.13), residues: 1168 loop : -1.12 (0.11), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.004 0.000 HIS G 38 PHE 0.018 0.001 PHE C 490 TYR 0.020 0.001 TYR B 501 ARG 0.002 0.000 ARG G 96 Details of bonding type rmsd hydrogen bonds : bond 0.23849 ( 1260) hydrogen bonds : angle 9.92792 ( 3528) SS BOND : bond 0.00277 ( 41) SS BOND : angle 0.72619 ( 82) covalent geometry : bond 0.00220 (32759) covalent geometry : angle 0.51369 (44569) *********************** 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 : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.6491 (mt) cc_final: 0.6281 (mt) REVERT: B 177 MET cc_start: -0.2333 (ttp) cc_final: -0.3229 (mmt) REVERT: B 293 LEU cc_start: 0.6839 (tp) cc_final: 0.6637 (tp) REVERT: C 534 VAL cc_start: 0.6460 (m) cc_final: 0.6101 (m) outliers start: 0 outliers final: 0 residues processed: 1051 average time/residue: 0.4831 time to fit residues: 790.4737 Evaluate side-chains 518 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 341 optimal weight: 20.0000 chunk 306 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 317 optimal weight: 0.7980 chunk 122 optimal weight: 0.0570 chunk 193 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 367 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 644 GLN A 751 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 787 GLN B 895 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1002 GLN B1071 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 487 ASN C 762 GLN C 787 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN C1071 GLN C1142 GLN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 39 GLN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.135700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.108784 restraints weight = 136413.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.110894 restraints weight = 79242.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.111735 restraints weight = 43224.334| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32800 Z= 0.140 Angle : 0.656 13.079 44651 Z= 0.339 Chirality : 0.046 0.268 5019 Planarity : 0.004 0.056 5758 Dihedral : 4.468 33.089 4389 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.57 % Favored : 97.38 % Rotamer: Outliers : 2.18 % Allowed : 10.11 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.12), residues: 4048 helix: 0.16 (0.18), residues: 689 sheet: 0.15 (0.14), residues: 1120 loop : -0.95 (0.12), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 110 HIS 0.008 0.001 HIS F 52 PHE 0.042 0.002 PHE C 855 TYR 0.030 0.002 TYR B1155 ARG 0.010 0.001 ARG B 815 Details of bonding type rmsd hydrogen bonds : bond 0.05210 ( 1260) hydrogen bonds : angle 6.86635 ( 3528) SS BOND : bond 0.00336 ( 41) SS BOND : angle 1.29876 ( 82) covalent geometry : bond 0.00303 (32759) covalent geometry : angle 0.65444 (44569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 571 time to evaluate : 3.748 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: A 153 MET cc_start: 0.2972 (ppp) cc_final: 0.2437 (pmm) REVERT: A 177 MET cc_start: 0.0486 (mmt) cc_final: 0.0022 (mmm) REVERT: A 239 GLN cc_start: 0.8782 (mt0) cc_final: 0.8383 (tp40) REVERT: A 269 TYR cc_start: 0.7269 (m-10) cc_final: 0.6860 (m-10) REVERT: A 287 ASP cc_start: 0.8628 (t0) cc_final: 0.8402 (t70) REVERT: A 316 SER cc_start: 0.8966 (t) cc_final: 0.8522 (m) REVERT: A 708 SER cc_start: 0.8277 (t) cc_final: 0.7662 (m) REVERT: A 900 MET cc_start: 0.7430 (mtt) cc_final: 0.6788 (mtp) REVERT: A 957 GLN cc_start: 0.8395 (tt0) cc_final: 0.8126 (tt0) REVERT: A 995 ARG cc_start: 0.8732 (mtp85) cc_final: 0.8479 (mtp85) REVERT: A 1042 PHE cc_start: 0.9126 (t80) cc_final: 0.8853 (t80) REVERT: B 55 PHE cc_start: 0.7723 (m-10) cc_final: 0.7364 (m-10) REVERT: B 128 ILE cc_start: 0.9159 (mm) cc_final: 0.8840 (mm) REVERT: B 177 MET cc_start: 0.1033 (ttp) cc_final: -0.0360 (mmt) REVERT: B 304 LYS cc_start: 0.9007 (tptt) cc_final: 0.8761 (tptt) REVERT: B 533 LEU cc_start: 0.5594 (tt) cc_final: 0.5175 (tp) REVERT: B 773 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7859 (mm-30) REVERT: B 858 LEU cc_start: 0.8349 (mm) cc_final: 0.7970 (tp) REVERT: B 902 MET cc_start: 0.9144 (tpp) cc_final: 0.8877 (tpp) REVERT: B 955 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7695 (t0) REVERT: B 995 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.7978 (mtm-85) REVERT: B 1018 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8639 (mt) REVERT: B 1111 GLU cc_start: 0.7977 (tt0) cc_final: 0.7477 (pp20) REVERT: C 54 LEU cc_start: 0.8392 (tp) cc_final: 0.8181 (tp) REVERT: C 195 LYS cc_start: 0.8810 (pttm) cc_final: 0.8088 (ptmm) REVERT: C 304 LYS cc_start: 0.8599 (mptt) cc_final: 0.8374 (mmtt) REVERT: C 429 PHE cc_start: 0.3179 (t80) cc_final: 0.2129 (t80) REVERT: C 489 TYR cc_start: 0.6145 (m-10) cc_final: 0.4652 (m-80) REVERT: C 564 GLN cc_start: 0.8564 (mt0) cc_final: 0.8061 (tp-100) REVERT: C 732 THR cc_start: 0.9251 (m) cc_final: 0.8884 (p) REVERT: C 859 THR cc_start: 0.8714 (m) cc_final: 0.8264 (p) REVERT: C 955 ASN cc_start: 0.8849 (m-40) cc_final: 0.6992 (m-40) REVERT: C 965 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8110 (tp40) REVERT: C 991 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8657 (p) REVERT: C 1014 ARG cc_start: 0.8486 (mmm-85) cc_final: 0.8126 (mmm-85) REVERT: C 1146 ASP cc_start: 0.8898 (t70) cc_final: 0.8620 (m-30) REVERT: D 36 TRP cc_start: 0.6597 (m100) cc_final: 0.6243 (m100) REVERT: D 63 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8711 (ptpt) REVERT: D 178 GLN cc_start: 0.5292 (OUTLIER) cc_final: 0.4836 (pm20) REVERT: F 36 TRP cc_start: 0.6625 (m100) cc_final: 0.6327 (m100) REVERT: F 46 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7776 (pm20) REVERT: F 64 PHE cc_start: 0.8519 (m-80) cc_final: 0.8218 (m-10) REVERT: G 40 TYR cc_start: 0.6932 (m-80) cc_final: 0.6687 (m-80) REVERT: G 49 LYS cc_start: 0.7929 (pttm) cc_final: 0.7214 (mmtm) REVERT: G 96 ARG cc_start: 0.7831 (tpt-90) cc_final: 0.7411 (tpp80) REVERT: G 167 TRP cc_start: 0.5323 (m100) cc_final: 0.4888 (m100) outliers start: 78 outliers final: 43 residues processed: 615 average time/residue: 0.4806 time to fit residues: 472.9689 Evaluate side-chains 493 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 445 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 PHE 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 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 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 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 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 758 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 991 VAL 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 331 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 352 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 232 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 275 optimal weight: 0.8980 chunk 370 optimal weight: 10.0000 chunk 225 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 207 HIS A 536 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 762 GLN A 913 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 165 ASN B 321 GLN B 655 HIS B 751 ASN B 901 GLN B 913 GLN B 925 ASN B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1088 HIS C 207 HIS C 239 GLN 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 C1071 GLN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN G 128 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.140192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.120768 restraints weight = 175660.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.121354 restraints weight = 109292.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.121925 restraints weight = 69263.700| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32800 Z= 0.163 Angle : 0.637 14.091 44651 Z= 0.328 Chirality : 0.045 0.210 5019 Planarity : 0.004 0.063 5758 Dihedral : 4.564 30.866 4389 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 2.99 % Allowed : 10.56 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 4048 helix: 0.61 (0.19), residues: 690 sheet: 0.34 (0.14), residues: 1125 loop : -0.90 (0.12), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 886 HIS 0.012 0.001 HIS C1048 PHE 0.029 0.002 PHE C 855 TYR 0.022 0.002 TYR B1155 ARG 0.013 0.001 ARG F 59 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 1260) hydrogen bonds : angle 6.18514 ( 3528) SS BOND : bond 0.00527 ( 41) SS BOND : angle 1.07220 ( 82) covalent geometry : bond 0.00362 (32759) covalent geometry : angle 0.63597 (44569) *********************** 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 578 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 471 time to evaluate : 3.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2534 (ppp) cc_final: 0.2048 (pmm) REVERT: A 177 MET cc_start: 0.0778 (mmt) cc_final: 0.0345 (mmm) REVERT: A 239 GLN cc_start: 0.8524 (mt0) cc_final: 0.8150 (tp40) REVERT: A 269 TYR cc_start: 0.7046 (m-10) cc_final: 0.6584 (m-80) REVERT: A 287 ASP cc_start: 0.8848 (t0) cc_final: 0.8619 (t70) REVERT: A 316 SER cc_start: 0.9038 (t) cc_final: 0.8564 (m) REVERT: A 708 SER cc_start: 0.8426 (t) cc_final: 0.7757 (m) REVERT: A 772 VAL cc_start: 0.9267 (t) cc_final: 0.9036 (p) REVERT: A 786 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8739 (mmmm) REVERT: A 957 GLN cc_start: 0.8595 (tt0) cc_final: 0.8053 (tp-100) REVERT: A 988 GLU cc_start: 0.8477 (mp0) cc_final: 0.8183 (pm20) REVERT: A 995 ARG cc_start: 0.9013 (mtp85) cc_final: 0.8798 (mtp85) REVERT: A 1002 GLN cc_start: 0.8947 (mt0) cc_final: 0.8691 (tt0) REVERT: A 1019 ARG cc_start: 0.8437 (tpt170) cc_final: 0.8049 (tpt-90) REVERT: B 177 MET cc_start: 0.0096 (ttp) cc_final: -0.0598 (mpp) REVERT: B 533 LEU cc_start: 0.6009 (tt) cc_final: 0.5477 (tp) REVERT: B 773 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8082 (mm-30) REVERT: B 902 MET cc_start: 0.9126 (tpp) cc_final: 0.8917 (tpp) REVERT: B 928 ASN cc_start: 0.8728 (m-40) cc_final: 0.8415 (m-40) REVERT: B 955 ASN cc_start: 0.8689 (m-40) cc_final: 0.8282 (t0) REVERT: B 966 LEU cc_start: 0.9248 (mt) cc_final: 0.8754 (tt) REVERT: B 995 ARG cc_start: 0.8655 (mtm-85) cc_final: 0.8217 (mtm-85) REVERT: B 1014 ARG cc_start: 0.8747 (tpp80) cc_final: 0.8512 (tpp80) REVERT: B 1018 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8678 (mt) REVERT: C 54 LEU cc_start: 0.8297 (tp) cc_final: 0.7967 (tp) REVERT: C 177 MET cc_start: 0.0422 (OUTLIER) cc_final: -0.0584 (mpp) REVERT: C 304 LYS cc_start: 0.8784 (mptt) cc_final: 0.8558 (mmtt) REVERT: C 401 VAL cc_start: 0.7279 (t) cc_final: 0.7022 (m) REVERT: C 564 GLN cc_start: 0.8694 (mt0) cc_final: 0.8066 (tp-100) REVERT: C 732 THR cc_start: 0.9371 (m) cc_final: 0.8977 (p) REVERT: C 765 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8090 (mtm110) REVERT: C 773 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8053 (mm-30) REVERT: C 774 GLN cc_start: 0.9018 (mt0) cc_final: 0.8801 (mt0) REVERT: C 775 ASP cc_start: 0.8553 (m-30) cc_final: 0.8072 (t70) REVERT: C 780 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6656 (mt-10) REVERT: C 859 THR cc_start: 0.9032 (m) cc_final: 0.8630 (p) REVERT: C 965 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8150 (tp-100) REVERT: C 1014 ARG cc_start: 0.8806 (mmm-85) cc_final: 0.8483 (mmm-85) REVERT: C 1146 ASP cc_start: 0.8824 (t70) cc_final: 0.8560 (m-30) REVERT: D 59 ARG cc_start: 0.6733 (mtm-85) cc_final: 0.6193 (mtm-85) REVERT: F 36 TRP cc_start: 0.6553 (m100) cc_final: 0.6193 (m100) REVERT: F 46 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7464 (pm20) REVERT: F 50 MET cc_start: 0.8784 (tpp) cc_final: 0.8409 (tpp) REVERT: G 40 TYR cc_start: 0.6521 (m-80) cc_final: 0.6207 (m-80) outliers start: 107 outliers final: 68 residues processed: 535 average time/residue: 0.4885 time to fit residues: 425.9455 Evaluate side-chains 469 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 398 time to evaluate : 4.356 ------------------------------------------------------------------------------- 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 172 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 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 730 SER Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 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 200 TYR Chi-restraints excluded: chain B residue 318 PHE 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 740 MET Chi-restraints excluded: chain B residue 750 SER 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 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 494 SER 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 765 ARG Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 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 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 82 VAL Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 128 GLN 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 316 optimal weight: 1.9990 chunk 389 optimal weight: 2.9990 chunk 357 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 379 optimal weight: 0.1980 chunk 23 optimal weight: 9.9990 chunk 365 optimal weight: 10.0000 chunk 285 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 391 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 271 GLN A 762 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 52 GLN C 607 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1159 HIS ** 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 128 GLN E 142 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.131163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.107417 restraints weight = 168668.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.107701 restraints weight = 103542.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.108426 restraints weight = 67330.080| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32800 Z= 0.162 Angle : 0.624 13.337 44651 Z= 0.322 Chirality : 0.045 0.266 5019 Planarity : 0.004 0.085 5758 Dihedral : 4.594 32.696 4389 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 2.71 % Allowed : 11.93 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.12), residues: 4048 helix: 0.83 (0.19), residues: 685 sheet: 0.31 (0.15), residues: 1101 loop : -0.90 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 886 HIS 0.007 0.001 HIS C1048 PHE 0.025 0.002 PHE C 306 TYR 0.020 0.002 TYR C1138 ARG 0.011 0.001 ARG A1014 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 1260) hydrogen bonds : angle 5.94494 ( 3528) SS BOND : bond 0.00305 ( 41) SS BOND : angle 1.07413 ( 82) covalent geometry : bond 0.00359 (32759) covalent geometry : angle 0.62336 (44569) *********************** 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 529 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 432 time to evaluate : 5.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1738 (ppp) cc_final: 0.1421 (pmm) REVERT: A 177 MET cc_start: 0.0513 (mmt) cc_final: 0.0245 (mmm) REVERT: A 269 TYR cc_start: 0.7417 (m-10) cc_final: 0.7058 (m-80) REVERT: A 304 LYS cc_start: 0.8985 (mttt) cc_final: 0.8500 (tppt) REVERT: A 368 LEU cc_start: 0.3386 (mt) cc_final: 0.2732 (pt) REVERT: A 699 LEU cc_start: 0.8604 (mm) cc_final: 0.8339 (mt) REVERT: A 708 SER cc_start: 0.8398 (t) cc_final: 0.7784 (m) REVERT: A 736 VAL cc_start: 0.8707 (t) cc_final: 0.8475 (p) REVERT: A 995 ARG cc_start: 0.9082 (mtp85) cc_final: 0.8865 (mtp85) REVERT: A 1017 GLU cc_start: 0.8568 (tp30) cc_final: 0.7920 (tm-30) REVERT: A 1019 ARG cc_start: 0.8448 (tpt170) cc_final: 0.8086 (tpt170) REVERT: B 177 MET cc_start: 0.0513 (ttp) cc_final: -0.0627 (mmp) REVERT: B 294 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8356 (p0) REVERT: B 304 LYS cc_start: 0.9441 (tppt) cc_final: 0.8562 (tptt) REVERT: B 695 TYR cc_start: 0.7077 (p90) cc_final: 0.6531 (p90) REVERT: B 928 ASN cc_start: 0.8744 (m-40) cc_final: 0.8457 (m-40) REVERT: B 955 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8324 (t0) REVERT: B 966 LEU cc_start: 0.9330 (mt) cc_final: 0.8786 (tt) REVERT: B 995 ARG cc_start: 0.8786 (mtm-85) cc_final: 0.8390 (mtm-85) REVERT: B 1014 ARG cc_start: 0.8759 (tpp80) cc_final: 0.8386 (tpp80) REVERT: C 54 LEU cc_start: 0.8489 (tp) cc_final: 0.8144 (tp) REVERT: C 177 MET cc_start: 0.0898 (OUTLIER) cc_final: 0.0216 (mtm) REVERT: C 195 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8681 (pttm) REVERT: C 304 LYS cc_start: 0.8989 (mptt) cc_final: 0.8663 (mmtt) REVERT: C 564 GLN cc_start: 0.8761 (mt0) cc_final: 0.7984 (tp-100) REVERT: C 732 THR cc_start: 0.9368 (m) cc_final: 0.9089 (p) REVERT: C 765 ARG cc_start: 0.8438 (mtm110) cc_final: 0.8123 (mtm-85) REVERT: C 773 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7992 (mm-30) REVERT: C 775 ASP cc_start: 0.8509 (m-30) cc_final: 0.8207 (t70) REVERT: C 859 THR cc_start: 0.9088 (m) cc_final: 0.8705 (p) REVERT: C 864 LEU cc_start: 0.8731 (tt) cc_final: 0.8466 (tt) REVERT: C 965 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8224 (tp40) REVERT: C 968 SER cc_start: 0.9256 (OUTLIER) cc_final: 0.8959 (p) REVERT: C 1002 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8425 (tm-30) REVERT: C 1146 ASP cc_start: 0.8862 (t70) cc_final: 0.8575 (m-30) REVERT: D 99 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7868 (mttm) REVERT: F 46 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7741 (pm20) REVERT: G 40 TYR cc_start: 0.6894 (m-80) cc_final: 0.6587 (m-80) outliers start: 97 outliers final: 63 residues processed: 493 average time/residue: 0.4850 time to fit residues: 390.1481 Evaluate side-chains 463 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 394 time to evaluate : 3.280 ------------------------------------------------------------------------------- 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 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 513 LEU 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 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU 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 294 ASP Chi-restraints excluded: chain B residue 315 THR 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 878 LEU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 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 730 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 981 LEU 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 D residue 66 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 115 LEU 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 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 279 optimal weight: 4.9990 chunk 381 optimal weight: 6.9990 chunk 274 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 337 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 272 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 245 HIS B 360 ASN B 532 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN C 913 GLN C1101 HIS ** 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** F 35 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** 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 = 0.4310 r_free = 0.4310 target = 0.122753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.096081 restraints weight = 156222.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.097868 restraints weight = 87131.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.099040 restraints weight = 57474.693| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.6652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 32800 Z= 0.298 Angle : 0.808 14.691 44651 Z= 0.424 Chirality : 0.050 0.290 5019 Planarity : 0.006 0.095 5758 Dihedral : 5.578 38.361 4389 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.37 % Favored : 95.58 % Rotamer: Outliers : 3.74 % Allowed : 12.21 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.12), residues: 4048 helix: 0.27 (0.18), residues: 710 sheet: -0.11 (0.15), residues: 1101 loop : -1.21 (0.12), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 39 HIS 0.011 0.002 HIS C1064 PHE 0.030 0.003 PHE C1109 TYR 0.035 0.003 TYR G 177 ARG 0.014 0.001 ARG A1014 Details of bonding type rmsd hydrogen bonds : bond 0.04959 ( 1260) hydrogen bonds : angle 6.51579 ( 3528) SS BOND : bond 0.00812 ( 41) SS BOND : angle 1.70986 ( 82) covalent geometry : bond 0.00668 (32759) covalent geometry : angle 0.80585 (44569) *********************** 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 529 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 395 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1335 (ppp) cc_final: 0.1035 (pmm) REVERT: A 177 MET cc_start: 0.1466 (mmp) cc_final: -0.0156 (mtp) REVERT: A 314 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8225 (tm-30) REVERT: A 1010 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8444 (tm-30) REVERT: A 1017 GLU cc_start: 0.8659 (tp30) cc_final: 0.8021 (tm-30) REVERT: A 1019 ARG cc_start: 0.8306 (tpt170) cc_final: 0.7990 (tpt170) REVERT: B 177 MET cc_start: -0.0527 (ttp) cc_final: -0.1459 (mmt) REVERT: B 294 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.7900 (p0) REVERT: B 304 LYS cc_start: 0.9478 (tppt) cc_final: 0.8784 (tptt) REVERT: B 380 TYR cc_start: 0.3368 (OUTLIER) cc_final: 0.2932 (m-80) REVERT: B 695 TYR cc_start: 0.7576 (p90) cc_final: 0.6270 (p90) REVERT: B 731 MET cc_start: 0.8622 (ptm) cc_final: 0.8012 (ptt) REVERT: B 765 ARG cc_start: 0.8568 (ptp90) cc_final: 0.8107 (ptp90) REVERT: B 902 MET cc_start: 0.9147 (tpp) cc_final: 0.8895 (tpp) REVERT: B 928 ASN cc_start: 0.8906 (m-40) cc_final: 0.8626 (m-40) REVERT: B 955 ASN cc_start: 0.8436 (m-40) cc_final: 0.8151 (t0) REVERT: B 966 LEU cc_start: 0.9303 (mt) cc_final: 0.8788 (tt) REVERT: B 995 ARG cc_start: 0.8739 (mtm-85) cc_final: 0.8450 (mtm-85) REVERT: B 1014 ARG cc_start: 0.8630 (tpp80) cc_final: 0.8258 (tpp80) REVERT: B 1023 ASN cc_start: 0.8937 (m-40) cc_final: 0.8479 (m110) REVERT: C 54 LEU cc_start: 0.8620 (tp) cc_final: 0.8206 (tp) REVERT: C 177 MET cc_start: 0.1240 (mtm) cc_final: 0.0340 (mtm) REVERT: C 304 LYS cc_start: 0.9048 (mptt) cc_final: 0.8798 (mmtt) REVERT: C 564 GLN cc_start: 0.8697 (mt0) cc_final: 0.8225 (tp-100) REVERT: C 729 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8979 (t) REVERT: C 752 LEU cc_start: 0.9467 (mt) cc_final: 0.9261 (mp) REVERT: C 755 GLN cc_start: 0.8892 (mt0) cc_final: 0.8586 (mt0) REVERT: C 762 GLN cc_start: 0.8446 (mm110) cc_final: 0.8144 (mm110) REVERT: C 765 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8239 (mtm-85) REVERT: C 773 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8100 (mm-30) REVERT: C 900 MET cc_start: 0.8795 (mmt) cc_final: 0.8583 (mmt) REVERT: C 965 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8423 (tp40) REVERT: C 1002 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8255 (tm-30) REVERT: C 1005 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7885 (tm-30) REVERT: F 81 MET cc_start: 0.6371 (tpp) cc_final: 0.5993 (tpp) REVERT: G 40 TYR cc_start: 0.6839 (m-80) cc_final: 0.6629 (m-10) outliers start: 134 outliers final: 95 residues processed: 487 average time/residue: 0.4097 time to fit residues: 327.6265 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 : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP 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 287 ASP 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 699 LEU 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 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 959 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 A residue 1129 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 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 934 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1010 GLN 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 C residue 58 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 730 SER 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 884 SER Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 934 ILE 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 15 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain F residue 71 THR 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 3 VAL Chi-restraints excluded: chain G residue 5 THR 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 248 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 327 optimal weight: 2.9990 chunk 381 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 169 optimal weight: 0.0170 chunk 113 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 281 optimal weight: 3.9990 chunk 335 optimal weight: 0.5980 chunk 215 optimal weight: 20.0000 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 784 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1023 ASN C 644 GLN C 935 GLN C1088 HIS ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS ** G 128 GLN ** 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 = 0.4392 r_free = 0.4392 target = 0.127835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.104326 restraints weight = 167398.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.105289 restraints weight = 104549.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.105471 restraints weight = 63149.530| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.6593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32800 Z= 0.123 Angle : 0.641 12.752 44651 Z= 0.325 Chirality : 0.046 0.323 5019 Planarity : 0.004 0.084 5758 Dihedral : 4.898 35.952 4389 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 2.51 % Allowed : 14.86 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.12), residues: 4048 helix: 0.69 (0.19), residues: 706 sheet: -0.00 (0.15), residues: 1104 loop : -1.12 (0.12), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 64 HIS 0.008 0.001 HIS C1083 PHE 0.029 0.002 PHE C 306 TYR 0.022 0.001 TYR D 109 ARG 0.008 0.001 ARG A1014 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 1260) hydrogen bonds : angle 5.86758 ( 3528) SS BOND : bond 0.00434 ( 41) SS BOND : angle 1.80985 ( 82) covalent geometry : bond 0.00274 (32759) covalent geometry : angle 0.63693 (44569) *********************** 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 494 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 404 time to evaluate : 3.403 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 153 MET cc_start: 0.1424 (ppp) cc_final: 0.1132 (pmm) REVERT: A 177 MET cc_start: 0.1227 (mmp) cc_final: -0.0582 (mtp) REVERT: A 708 SER cc_start: 0.8393 (t) cc_final: 0.7863 (m) REVERT: A 1017 GLU cc_start: 0.8449 (tp30) cc_final: 0.7827 (tm-30) REVERT: A 1019 ARG cc_start: 0.8307 (tpt170) cc_final: 0.7959 (tpt-90) REVERT: B 177 MET cc_start: 0.0220 (ttp) cc_final: -0.0895 (mmt) REVERT: B 278 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.6919 (mptt) REVERT: B 294 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8082 (p0) REVERT: B 304 LYS cc_start: 0.9451 (tppt) cc_final: 0.8703 (tptt) REVERT: B 501 TYR cc_start: 0.4757 (m-80) cc_final: 0.4387 (m-80) REVERT: B 695 TYR cc_start: 0.7438 (p90) cc_final: 0.6451 (p90) REVERT: B 765 ARG cc_start: 0.8658 (ptp90) cc_final: 0.8229 (ptp90) REVERT: B 900 MET cc_start: 0.8073 (mtt) cc_final: 0.7451 (mmt) REVERT: B 928 ASN cc_start: 0.8815 (m-40) cc_final: 0.8469 (m-40) REVERT: B 955 ASN cc_start: 0.8350 (m-40) cc_final: 0.8069 (t0) REVERT: B 966 LEU cc_start: 0.9326 (mt) cc_final: 0.8735 (tt) REVERT: B 995 ARG cc_start: 0.8809 (mtm-85) cc_final: 0.8441 (mtm-85) REVERT: B 1014 ARG cc_start: 0.8547 (tpp80) cc_final: 0.8104 (tpp80) REVERT: C 54 LEU cc_start: 0.8589 (tp) cc_final: 0.8158 (tp) REVERT: C 153 MET cc_start: 0.7382 (mmt) cc_final: 0.7118 (mmm) REVERT: C 177 MET cc_start: 0.2062 (mtm) cc_final: 0.1248 (mtm) REVERT: C 304 LYS cc_start: 0.9121 (mptt) cc_final: 0.8866 (mmtt) REVERT: C 543 PHE cc_start: 0.6882 (m-10) cc_final: 0.6647 (m-80) REVERT: C 564 GLN cc_start: 0.8684 (mt0) cc_final: 0.8155 (tp-100) REVERT: C 762 GLN cc_start: 0.8225 (mm110) cc_final: 0.7892 (mm110) REVERT: C 765 ARG cc_start: 0.8522 (mtm110) cc_final: 0.8278 (mtm110) REVERT: C 773 GLU cc_start: 0.8232 (mm-30) cc_final: 0.8025 (mm-30) REVERT: C 790 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8269 (mtmm) REVERT: C 965 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8283 (tp40) REVERT: C 995 ARG cc_start: 0.9075 (mtm180) cc_final: 0.8626 (mtm180) REVERT: C 1002 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8302 (tm-30) REVERT: C 1092 GLU cc_start: 0.8081 (pm20) cc_final: 0.7427 (pm20) REVERT: C 1125 ASN cc_start: 0.7742 (p0) cc_final: 0.7293 (m-40) REVERT: F 81 MET cc_start: 0.6498 (tpp) cc_final: 0.6216 (tpp) REVERT: G 40 TYR cc_start: 0.7110 (m-80) cc_final: 0.6846 (m-10) outliers start: 90 outliers final: 63 residues processed: 456 average time/residue: 0.4393 time to fit residues: 325.3265 Evaluate side-chains 425 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 360 time to evaluate : 3.394 ------------------------------------------------------------------------------- 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 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 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 762 GLN 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 994 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 294 ASP 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 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 822 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 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 58 PHE 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 401 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 922 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 66 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 LYS 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 E residue 15 LEU Chi-restraints excluded: chain F residue 71 THR 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 151 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 6 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 356 optimal weight: 0.9990 chunk 312 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 275 optimal weight: 0.1980 chunk 301 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 856 ASN B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 955 ASN ** 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 = 0.4373 r_free = 0.4373 target = 0.126601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.103954 restraints weight = 169312.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.104355 restraints weight = 108392.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.104301 restraints weight = 77535.929| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.6869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 32800 Z= 0.151 Angle : 0.649 13.092 44651 Z= 0.330 Chirality : 0.046 0.350 5019 Planarity : 0.004 0.120 5758 Dihedral : 4.883 34.922 4389 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.05 % Rotamer: Outliers : 2.65 % Allowed : 15.36 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 4048 helix: 0.66 (0.19), residues: 717 sheet: 0.00 (0.15), residues: 1109 loop : -1.11 (0.12), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 886 HIS 0.004 0.001 HIS E 94 PHE 0.030 0.002 PHE B 306 TYR 0.021 0.002 TYR B 204 ARG 0.010 0.001 ARG B 44 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 1260) hydrogen bonds : angle 5.83047 ( 3528) SS BOND : bond 0.00326 ( 41) SS BOND : angle 1.45941 ( 82) covalent geometry : bond 0.00339 (32759) covalent geometry : angle 0.64705 (44569) *********************** 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 469 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 374 time to evaluate : 3.798 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: A 153 MET cc_start: 0.1262 (ppp) cc_final: 0.0999 (pmm) REVERT: A 177 MET cc_start: 0.1172 (mmp) cc_final: -0.0491 (mtp) REVERT: A 304 LYS cc_start: 0.9114 (mttt) cc_final: 0.8776 (tppt) REVERT: A 314 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8030 (tm-30) REVERT: A 708 SER cc_start: 0.8432 (t) cc_final: 0.7889 (m) REVERT: A 957 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 995 ARG cc_start: 0.9007 (mtp85) cc_final: 0.8773 (mtm-85) REVERT: A 1017 GLU cc_start: 0.8503 (tp30) cc_final: 0.8003 (tm-30) REVERT: A 1019 ARG cc_start: 0.8272 (tpt170) cc_final: 0.7981 (tpt-90) REVERT: B 177 MET cc_start: 0.0412 (ttp) cc_final: -0.0727 (mmt) REVERT: B 294 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8013 (p0) REVERT: B 304 LYS cc_start: 0.9455 (tppt) cc_final: 0.8759 (tptt) REVERT: B 765 ARG cc_start: 0.8638 (ptp90) cc_final: 0.8170 (ptp90) REVERT: B 900 MET cc_start: 0.8080 (mtt) cc_final: 0.7841 (mmt) REVERT: B 928 ASN cc_start: 0.8838 (m-40) cc_final: 0.8501 (m-40) REVERT: B 966 LEU cc_start: 0.9312 (mt) cc_final: 0.8766 (tt) REVERT: B 983 ARG cc_start: 0.7923 (mtm180) cc_final: 0.7604 (tpt90) REVERT: B 995 ARG cc_start: 0.8767 (mtm-85) cc_final: 0.8431 (mtm-85) REVERT: B 1014 ARG cc_start: 0.8505 (tpp80) cc_final: 0.8128 (tpp80) REVERT: B 1042 PHE cc_start: 0.8417 (t80) cc_final: 0.8212 (t80) REVERT: C 54 LEU cc_start: 0.8641 (tp) cc_final: 0.8239 (tp) REVERT: C 153 MET cc_start: 0.7557 (mmt) cc_final: 0.7350 (mmm) REVERT: C 177 MET cc_start: 0.1705 (mtm) cc_final: 0.0893 (mtm) REVERT: C 287 ASP cc_start: 0.8067 (t0) cc_final: 0.7839 (t0) REVERT: C 306 PHE cc_start: 0.7792 (t80) cc_final: 0.7266 (t80) REVERT: C 762 GLN cc_start: 0.8282 (mm110) cc_final: 0.7973 (mm110) REVERT: C 773 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8035 (mm-30) REVERT: C 790 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8664 (mtpt) REVERT: C 868 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7529 (tp30) REVERT: C 911 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8584 (p) REVERT: C 957 GLN cc_start: 0.8544 (tp-100) cc_final: 0.8235 (tp-100) REVERT: C 965 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8419 (tp40) REVERT: C 1002 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8583 (tm-30) REVERT: D 99 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7974 (mmmt) REVERT: F 81 MET cc_start: 0.6630 (tpp) cc_final: 0.6327 (tpp) REVERT: F 89 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7587 (tm-30) REVERT: G 40 TYR cc_start: 0.7274 (m-80) cc_final: 0.6981 (m-10) outliers start: 95 outliers final: 71 residues processed: 437 average time/residue: 0.4298 time to fit residues: 307.7900 Evaluate side-chains 423 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 349 time to evaluate : 3.913 ------------------------------------------------------------------------------- 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 513 LEU 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 730 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 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 585 LEU 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 934 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 922 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 66 ASP Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 LYS 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 F residue 50 MET Chi-restraints excluded: chain F residue 71 THR 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 107 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 278 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 329 optimal weight: 6.9990 chunk 319 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 108 optimal weight: 0.1980 chunk 106 optimal weight: 2.9990 chunk 369 optimal weight: 4.9990 chunk 370 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 856 ASN B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** 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 = 0.4366 r_free = 0.4366 target = 0.126241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.103674 restraints weight = 169373.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.103915 restraints weight = 105968.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.104279 restraints weight = 68365.035| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 32800 Z= 0.147 Angle : 0.649 12.376 44651 Z= 0.330 Chirality : 0.046 0.289 5019 Planarity : 0.004 0.073 5758 Dihedral : 4.859 33.926 4389 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.10 % Favored : 95.85 % Rotamer: Outliers : 2.54 % Allowed : 15.50 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 4048 helix: 0.68 (0.19), residues: 711 sheet: 0.11 (0.15), residues: 1097 loop : -1.13 (0.12), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 886 HIS 0.004 0.001 HIS E 94 PHE 0.034 0.002 PHE A 497 TYR 0.019 0.001 TYR B 170 ARG 0.006 0.001 ARG A1014 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 1260) hydrogen bonds : angle 5.82177 ( 3528) SS BOND : bond 0.00358 ( 41) SS BOND : angle 1.75000 ( 82) covalent geometry : bond 0.00336 (32759) covalent geometry : angle 0.64551 (44569) *********************** 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 468 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 377 time to evaluate : 3.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1302 (mmp) cc_final: -0.0248 (mtp) REVERT: A 304 LYS cc_start: 0.9097 (mttt) cc_final: 0.8751 (tppt) REVERT: A 708 SER cc_start: 0.8456 (t) cc_final: 0.7920 (m) REVERT: A 957 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8079 (tm-30) REVERT: A 995 ARG cc_start: 0.9017 (mtp85) cc_final: 0.8776 (mtm-85) REVERT: A 1017 GLU cc_start: 0.8508 (tp30) cc_final: 0.8049 (tm-30) REVERT: B 177 MET cc_start: 0.0559 (ttp) cc_final: -0.0789 (mmt) REVERT: B 294 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8086 (p0) REVERT: B 765 ARG cc_start: 0.8630 (ptp90) cc_final: 0.8217 (ptp90) REVERT: B 900 MET cc_start: 0.8077 (mtt) cc_final: 0.7349 (mmt) REVERT: B 928 ASN cc_start: 0.8804 (m-40) cc_final: 0.8472 (m-40) REVERT: B 966 LEU cc_start: 0.9290 (mt) cc_final: 0.8761 (tt) REVERT: B 1014 ARG cc_start: 0.8488 (tpp80) cc_final: 0.8078 (tpp80) REVERT: B 1042 PHE cc_start: 0.8437 (t80) cc_final: 0.8223 (t80) REVERT: B 1045 LYS cc_start: 0.8304 (tptt) cc_final: 0.7966 (tppp) REVERT: C 50 SER cc_start: 0.9436 (m) cc_final: 0.9082 (p) REVERT: C 54 LEU cc_start: 0.8714 (tp) cc_final: 0.8262 (tp) REVERT: C 177 MET cc_start: 0.1813 (mtm) cc_final: 0.1155 (mtm) REVERT: C 699 LEU cc_start: 0.8599 (mt) cc_final: 0.7959 (mt) REVERT: C 755 GLN cc_start: 0.8872 (mt0) cc_final: 0.8311 (tt0) REVERT: C 764 ASN cc_start: 0.8652 (m-40) cc_final: 0.8428 (m110) REVERT: C 790 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8680 (mtpt) REVERT: C 911 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8606 (p) REVERT: C 965 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8421 (tp40) REVERT: C 1086 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8157 (pttm) REVERT: C 1092 GLU cc_start: 0.8038 (pm20) cc_final: 0.7206 (pm20) REVERT: F 81 MET cc_start: 0.6505 (tpp) cc_final: 0.6181 (tpp) REVERT: F 89 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7320 (tm-30) REVERT: G 40 TYR cc_start: 0.7030 (m-80) cc_final: 0.6779 (m-10) REVERT: G 90 TYR cc_start: 0.7331 (m-80) cc_final: 0.6839 (m-80) outliers start: 91 outliers final: 76 residues processed: 439 average time/residue: 0.4266 time to fit residues: 306.0310 Evaluate side-chains 437 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 358 time to evaluate : 3.610 ------------------------------------------------------------------------------- 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 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 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 294 ASP 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 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 926 GLN 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 B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 730 SER 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 968 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1086 LYS 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 99 LYS 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 F residue 71 THR 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 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 49 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 358 optimal weight: 10.0000 chunk 269 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 355 optimal weight: 20.0000 chunk 324 optimal weight: 7.9990 chunk 285 optimal weight: 2.9990 chunk 290 optimal weight: 5.9990 chunk 204 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 774 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 856 ASN B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 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 = 0.4311 r_free = 0.4311 target = 0.122582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.096122 restraints weight = 158110.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.098078 restraints weight = 85343.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.099369 restraints weight = 55308.884| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.7617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 32800 Z= 0.211 Angle : 0.719 12.834 44651 Z= 0.369 Chirality : 0.047 0.279 5019 Planarity : 0.005 0.049 5758 Dihedral : 5.223 35.912 4389 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.11 % Favored : 94.84 % Rotamer: Outliers : 2.65 % Allowed : 15.89 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.13), residues: 4048 helix: 0.50 (0.19), residues: 707 sheet: -0.06 (0.15), residues: 1087 loop : -1.20 (0.12), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 886 HIS 0.006 0.001 HIS A 207 PHE 0.034 0.002 PHE A 497 TYR 0.022 0.002 TYR C 449 ARG 0.013 0.001 ARG B 509 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 1260) hydrogen bonds : angle 6.15173 ( 3528) SS BOND : bond 0.00437 ( 41) SS BOND : angle 1.55162 ( 82) covalent geometry : bond 0.00475 (32759) covalent geometry : angle 0.71637 (44569) *********************** 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 455 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 360 time to evaluate : 3.420 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: A 177 MET cc_start: 0.1807 (mmp) cc_final: 0.0128 (mtp) REVERT: A 731 MET cc_start: 0.8949 (ptm) cc_final: 0.8216 (ppp) REVERT: A 759 PHE cc_start: 0.7620 (t80) cc_final: 0.7012 (t80) REVERT: A 957 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8067 (tm-30) REVERT: A 995 ARG cc_start: 0.8959 (mtp85) cc_final: 0.8744 (mtm-85) REVERT: A 1017 GLU cc_start: 0.8571 (tp30) cc_final: 0.8173 (tm-30) REVERT: B 177 MET cc_start: -0.0078 (ttp) cc_final: -0.0940 (mpp) REVERT: B 294 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8251 (p0) REVERT: B 356 LYS cc_start: 0.6774 (mttt) cc_final: 0.6433 (tppt) REVERT: B 765 ARG cc_start: 0.8582 (ptp90) cc_final: 0.8131 (ptp90) REVERT: B 928 ASN cc_start: 0.8801 (m-40) cc_final: 0.8445 (m-40) REVERT: B 966 LEU cc_start: 0.9287 (mt) cc_final: 0.8752 (tt) REVERT: B 995 ARG cc_start: 0.8687 (mtm-85) cc_final: 0.8449 (ttp-170) REVERT: B 1014 ARG cc_start: 0.8544 (tpp80) cc_final: 0.8220 (tpp80) REVERT: B 1017 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7782 (tp30) REVERT: B 1045 LYS cc_start: 0.8419 (tptt) cc_final: 0.8029 (tppp) REVERT: C 50 SER cc_start: 0.9395 (m) cc_final: 0.9044 (p) REVERT: C 54 LEU cc_start: 0.8716 (tp) cc_final: 0.8254 (tp) REVERT: C 177 MET cc_start: 0.1898 (mtm) cc_final: 0.1460 (mtm) REVERT: C 699 LEU cc_start: 0.8628 (mt) cc_final: 0.8045 (mt) REVERT: C 729 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8862 (t) REVERT: C 755 GLN cc_start: 0.8862 (mt0) cc_final: 0.8618 (tt0) REVERT: C 764 ASN cc_start: 0.8740 (m-40) cc_final: 0.8526 (m110) REVERT: C 911 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8906 (p) REVERT: C 965 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8484 (tp40) REVERT: C 1002 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8219 (tm-30) REVERT: C 1005 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7701 (tm-30) REVERT: C 1086 LYS cc_start: 0.8441 (pttt) cc_final: 0.8138 (pttm) REVERT: F 155 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7523 (mm-30) REVERT: G 90 TYR cc_start: 0.7133 (m-80) cc_final: 0.6637 (m-80) outliers start: 95 outliers final: 82 residues processed: 423 average time/residue: 0.4375 time to fit residues: 300.5332 Evaluate side-chains 426 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 340 time to evaluate : 3.684 ------------------------------------------------------------------------------- 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 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 595 VAL 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 777 ASN 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 954 GLN Chi-restraints excluded: chain A residue 959 LEU 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 128 ILE Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 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 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 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 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 468 ILE 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 724 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 730 SER 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 968 SER 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 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 F residue 71 THR 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 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 223 optimal weight: 20.0000 chunk 340 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 374 optimal weight: 5.9990 chunk 372 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 386 optimal weight: 9.9990 chunk 366 optimal weight: 5.9990 chunk 254 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 318 optimal weight: 10.0000 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 ASN B 196 ASN B 474 GLN B 644 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 394 ASN C 487 ASN C 544 ASN C 613 GLN C 913 GLN C1058 HIS ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN F 178 GLN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.116915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.092492 restraints weight = 156699.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.093996 restraints weight = 93548.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.094888 restraints weight = 63863.471| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.8907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.136 32800 Z= 0.386 Angle : 0.969 15.687 44651 Z= 0.509 Chirality : 0.055 0.375 5019 Planarity : 0.007 0.078 5758 Dihedral : 6.753 47.343 4389 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 28.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.26 % Favored : 92.71 % Rotamer: Outliers : 2.96 % Allowed : 16.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.12), residues: 4048 helix: -0.43 (0.17), residues: 729 sheet: -0.54 (0.15), residues: 1080 loop : -1.70 (0.12), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP D 36 HIS 0.014 0.002 HIS G 38 PHE 0.041 0.004 PHE B1042 TYR 0.029 0.003 TYR B 473 ARG 0.015 0.001 ARG A 765 Details of bonding type rmsd hydrogen bonds : bond 0.05626 ( 1260) hydrogen bonds : angle 7.28391 ( 3528) SS BOND : bond 0.00611 ( 41) SS BOND : angle 2.24863 ( 82) covalent geometry : bond 0.00860 (32759) covalent geometry : angle 0.96523 (44569) ********************** 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 446 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 340 time to evaluate : 3.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.2201 (mmp) cc_final: -0.0059 (ttt) REVERT: A 303 LEU cc_start: 0.9573 (tp) cc_final: 0.9304 (tt) REVERT: A 957 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8330 (tm-30) REVERT: A 1017 GLU cc_start: 0.8836 (tp30) cc_final: 0.8362 (tm-30) REVERT: B 153 MET cc_start: 0.6430 (ppp) cc_final: 0.5914 (ppp) REVERT: B 177 MET cc_start: -0.1222 (ttp) cc_final: -0.2074 (mmt) REVERT: B 195 LYS cc_start: 0.8182 (ptmt) cc_final: 0.7581 (pttm) REVERT: B 294 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8171 (p0) REVERT: B 765 ARG cc_start: 0.8854 (ptp90) cc_final: 0.8243 (ptp90) REVERT: B 966 LEU cc_start: 0.9507 (mt) cc_final: 0.8893 (tt) REVERT: B 980 ILE cc_start: 0.9713 (OUTLIER) cc_final: 0.9468 (mp) REVERT: B 995 ARG cc_start: 0.9041 (mtm-85) cc_final: 0.8778 (ttp-170) REVERT: B 1014 ARG cc_start: 0.8828 (tpp80) cc_final: 0.8467 (tpp80) REVERT: C 54 LEU cc_start: 0.8978 (tp) cc_final: 0.8574 (tp) REVERT: C 177 MET cc_start: 0.1914 (mtm) cc_final: 0.1590 (mtm) REVERT: C 729 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8950 (t) REVERT: C 763 LEU cc_start: 0.9576 (mt) cc_final: 0.9357 (mp) REVERT: C 765 ARG cc_start: 0.8504 (mtm110) cc_final: 0.8182 (mtm110) REVERT: C 790 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8532 (mtmm) REVERT: C 911 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.9001 (p) REVERT: C 965 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8642 (tp40) REVERT: C 978 ASN cc_start: 0.9170 (OUTLIER) cc_final: 0.8613 (p0) REVERT: C 1086 LYS cc_start: 0.8356 (pttt) cc_final: 0.7896 (pttm) REVERT: D 99 LYS cc_start: 0.8131 (mmtt) cc_final: 0.7556 (mtmm) REVERT: D 107 PHE cc_start: 0.8766 (m-10) cc_final: 0.8237 (m-80) REVERT: F 11 LEU cc_start: 0.4879 (tp) cc_final: 0.4599 (tp) REVERT: F 29 PHE cc_start: 0.6326 (t80) cc_final: 0.5923 (t80) REVERT: F 57 GLU cc_start: 0.8857 (tt0) cc_final: 0.8576 (tt0) REVERT: F 81 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.5915 (tpp) REVERT: G 90 TYR cc_start: 0.7336 (m-80) cc_final: 0.6849 (m-80) outliers start: 106 outliers final: 81 residues processed: 420 average time/residue: 0.4245 time to fit residues: 290.7610 Evaluate side-chains 397 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 310 time to evaluate : 4.348 ------------------------------------------------------------------------------- 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 276 LEU Chi-restraints excluded: chain A residue 315 THR 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 699 LEU Chi-restraints excluded: chain A residue 729 VAL 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 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 954 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 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 772 VAL 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 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 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1065 VAL 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 385 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 934 ILE 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 990 GLU 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 21 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 MET 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 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 360 optimal weight: 20.0000 chunk 165 optimal weight: 0.2980 chunk 207 optimal weight: 0.7980 chunk 318 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 277 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 292 optimal weight: 0.0670 overall best weight: 1.4320 ------------------------------------------------------------------------------- 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 563 GLN A 580 GLN A 872 GLN B 474 GLN 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** C 564 GLN C 613 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1135 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.122172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.099376 restraints weight = 168012.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.100944 restraints weight = 100086.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.101704 restraints weight = 57809.363| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.8729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32800 Z= 0.170 Angle : 0.748 14.010 44651 Z= 0.382 Chirality : 0.049 0.300 5019 Planarity : 0.005 0.071 5758 Dihedral : 5.792 44.667 4389 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 2.23 % Allowed : 17.71 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.12), residues: 4048 helix: 0.16 (0.18), residues: 713 sheet: -0.44 (0.15), residues: 1060 loop : -1.51 (0.12), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 258 HIS 0.006 0.001 HIS E 94 PHE 0.040 0.002 PHE B 562 TYR 0.019 0.002 TYR C 269 ARG 0.018 0.001 ARG A 765 Details of bonding type rmsd hydrogen bonds : bond 0.04289 ( 1260) hydrogen bonds : angle 6.47070 ( 3528) SS BOND : bond 0.00672 ( 41) SS BOND : angle 1.84968 ( 82) covalent geometry : bond 0.00382 (32759) covalent geometry : angle 0.74491 (44569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14137.60 seconds wall clock time: 252 minutes 10.17 seconds (15130.17 seconds total)