Starting phenix.real_space_refine on Fri Mar 6 20:30:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dk4_30702/03_2026/7dk4_30702.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dk4_30702/03_2026/7dk4_30702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dk4_30702/03_2026/7dk4_30702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dk4_30702/03_2026/7dk4_30702.map" model { file = "/net/cci-nas-00/data/ceres_data/7dk4_30702/03_2026/7dk4_30702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dk4_30702/03_2026/7dk4_30702.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.084 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 159 5.16 5 C 22017 2.51 5 N 5805 2.21 5 O 6726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34707 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "b" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1686 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 8, 'TRANS': 204} Chain: "A" Number of atoms: 8280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8280 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 51, 'TRANS': 1006} Chain breaks: 6 Chain: "B" Number of atoms: 8280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8280 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 51, 'TRANS': 1006} Chain breaks: 6 Chain: "C" Number of atoms: 8280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8280 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 51, 'TRANS': 1006} Chain breaks: 6 Chain: "c" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "d" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1686 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 8, 'TRANS': 204} Chain: "e" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "f" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1686 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 8, 'TRANS': 204} Time building chain proxies: 8.04, per 1000 atoms: 0.23 Number of scatterers: 34707 At special positions: 0 Unit cell: (148.92, 161.16, 234.6, 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 159 16.00 O 6726 8.00 N 5805 7.00 C 22017 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 95 " distance=2.03 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 199 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 92 " distance=2.03 Simple disulfide: pdb=" SG CYS b 138 " - pdb=" SG CYS b 198 " distance=2.03 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 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " 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 c 22 " - pdb=" SG CYS c 95 " distance=2.03 Simple disulfide: pdb=" SG CYS c 144 " - pdb=" SG CYS c 199 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 92 " distance=2.03 Simple disulfide: pdb=" SG CYS d 138 " - pdb=" SG CYS d 198 " distance=2.03 Simple disulfide: pdb=" SG CYS e 22 " - pdb=" SG CYS e 95 " distance=2.03 Simple disulfide: pdb=" SG CYS e 144 " - pdb=" SG CYS e 199 " distance=2.03 Simple disulfide: pdb=" SG CYS f 23 " - pdb=" SG CYS f 92 " distance=2.03 Simple disulfide: pdb=" SG CYS f 138 " - pdb=" SG CYS f 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.8 seconds 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8364 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 77 sheets defined 17.9% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'a' and resid 86 through 90 removed outlier: 3.685A pdb=" N THR a 90 " --> pdb=" O THR a 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 131 Processing helix chain 'b' and resid 187 through 191 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.506A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.628A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.104A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.570A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.560A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.055A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.675A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.607A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) 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 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.801A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.648A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.745A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (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 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 984 removed outlier: 3.550A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1031 removed outlier: 4.677A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.503A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.598A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 782 removed outlier: 4.122A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.746A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.341A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.521A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (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 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: 3.567A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.477A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.697A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.600A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.539A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.696A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.543A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.530A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.723A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.861A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'c' and resid 190 through 192 No H-bonds generated for 'chain 'c' and resid 190 through 192' Processing helix chain 'd' and resid 125 through 132 Processing helix chain 'd' and resid 187 through 191 Processing helix chain 'e' and resid 86 through 90 Processing helix chain 'f' and resid 125 through 132 Processing helix chain 'f' and resid 187 through 191 Processing sheet with id=AA1, first strand: chain 'a' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'a' and resid 57 through 59 removed outlier: 3.621A pdb=" N ALA a 96 " --> pdb=" O HIS a 35 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE a 106 " --> pdb=" O LYS a 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 57 through 59 removed outlier: 3.621A pdb=" N ALA a 96 " --> pdb=" O HIS a 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 125 through 128 removed outlier: 6.087A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 125 through 128 removed outlier: 6.087A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU a 178 " --> pdb=" O GLN a 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 155 through 158 removed outlier: 4.730A pdb=" N VAL a 197 " --> pdb=" O ILE a 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 5 through 7 removed outlier: 3.680A pdb=" N ILE b 79 " --> pdb=" O ALA b 19 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE b 21 " --> pdb=" O LEU b 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 10 through 13 removed outlier: 6.456A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA b 88 " --> pdb=" O LEU b 108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 49 through 52 removed outlier: 6.106A pdb=" N LEU b 50 " --> pdb=" O GLN b 41 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN b 41 " --> pdb=" O LEU b 50 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE b 52 " --> pdb=" O TRP b 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 121 through 122 removed outlier: 3.553A pdb=" N LEU b 140 " --> pdb=" O MET b 179 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR b 177 " --> pdb=" O ASN b 142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER b 178 " --> pdb=" O THR b 168 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR b 182 " --> pdb=" O LEU b 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 158 through 159 removed outlier: 3.774A pdb=" N TRP b 152 " --> pdb=" O ARG b 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.531A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.029A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS B 537 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.518A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.793A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.981A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.381A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 326 through 327 removed outlier: 3.926A pdb=" N LYS A 537 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.663A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.067A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.156A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.156A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AC8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.554A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AD1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.921A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 5.269A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AD4, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.693A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.644A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.812A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.712A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.422A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 311 through 316 removed outlier: 5.255A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.699A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.466A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.136A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'B' and resid 788 through 790 removed outlier: 6.242A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.005A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.725A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.210A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 153 through 157 removed outlier: 6.370A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR C 259 " --> pdb=" O HIS C 245 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.318A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.670A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.831A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.991A 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: 3.598A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.534A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.622A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG4, first strand: chain 'c' and resid 6 through 7 removed outlier: 5.946A pdb=" N GLN c 16 " --> pdb=" O SER c 84 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'c' and resid 57 through 58 removed outlier: 6.784A pdb=" N TRP c 36 " --> pdb=" O LEU c 48 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL c 50 " --> pdb=" O VAL c 34 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL c 34 " --> pdb=" O VAL c 50 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA c 96 " --> pdb=" O HIS c 35 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL c 37 " --> pdb=" O TYR c 94 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N CYS c 95 " --> pdb=" O TRP c 107 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP c 107 " --> pdb=" O CYS c 95 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS c 97 " --> pdb=" O ASP c 105 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 57 through 58 removed outlier: 6.784A pdb=" N TRP c 36 " --> pdb=" O LEU c 48 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL c 50 " --> pdb=" O VAL c 34 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL c 34 " --> pdb=" O VAL c 50 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA c 96 " --> pdb=" O HIS c 35 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL c 37 " --> pdb=" O TYR c 94 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'c' and resid 124 through 128 removed outlier: 3.707A pdb=" N LYS c 147 " --> pdb=" O SER c 124 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY c 143 " --> pdb=" O LEU c 128 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS c 144 " --> pdb=" O SER c 183 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER c 183 " --> pdb=" O CYS c 144 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER c 184 " --> pdb=" O HIS c 168 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'c' and resid 124 through 128 removed outlier: 3.707A pdb=" N LYS c 147 " --> pdb=" O SER c 124 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY c 143 " --> pdb=" O LEU c 128 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR c 179 " --> pdb=" O GLY c 148 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU c 178 " --> pdb=" O GLN c 175 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'c' and resid 155 through 158 Processing sheet with id=AH1, first strand: chain 'd' and resid 6 through 7 Processing sheet with id=AH2, first strand: chain 'd' and resid 10 through 14 removed outlier: 6.373A pdb=" N LEU d 11 " --> pdb=" O GLU d 109 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS d 111 " --> pdb=" O LEU d 11 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL d 13 " --> pdb=" O LYS d 111 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS d 38 " --> pdb=" O GLN d 93 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE d 52 " --> pdb=" O TRP d 39 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN d 41 " --> pdb=" O LEU d 50 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU d 50 " --> pdb=" O GLN d 41 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LYS d 43 " --> pdb=" O PRO d 48 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN d 57 " --> pdb=" O TYR d 53 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'd' and resid 120 through 122 removed outlier: 4.384A pdb=" N SER d 120 " --> pdb=" O PHE d 139 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL d 136 " --> pdb=" O LEU d 183 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYR d 177 " --> pdb=" O ASN d 142 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU d 164 " --> pdb=" O THR d 182 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'd' and resid 148 through 153 removed outlier: 3.859A pdb=" N GLU d 199 " --> pdb=" O LYS d 151 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS d 153 " --> pdb=" O THR d 197 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR d 197 " --> pdb=" O LYS d 153 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'e' and resid 6 through 7 removed outlier: 3.693A pdb=" N MET e 82 " --> pdb=" O LEU e 18 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'e' and resid 57 through 59 removed outlier: 7.034A pdb=" N TRP e 36 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA e 96 " --> pdb=" O HIS e 35 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N CYS e 95 " --> pdb=" O TRP e 107 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TRP e 107 " --> pdb=" O CYS e 95 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS e 97 " --> pdb=" O ASP e 105 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'e' and resid 57 through 59 removed outlier: 7.034A pdb=" N TRP e 36 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA e 96 " --> pdb=" O HIS e 35 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'e' and resid 124 through 128 removed outlier: 3.842A pdb=" N LYS e 147 " --> pdb=" O SER e 124 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY e 143 " --> pdb=" O LEU e 128 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N CYS e 144 " --> pdb=" O SER e 183 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR e 179 " --> pdb=" O GLY e 148 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'e' and resid 124 through 128 removed outlier: 3.842A pdb=" N LYS e 147 " --> pdb=" O SER e 124 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY e 143 " --> pdb=" O LEU e 128 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N CYS e 144 " --> pdb=" O SER e 183 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR e 179 " --> pdb=" O GLY e 148 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'e' and resid 155 through 158 Processing sheet with id=AI2, first strand: chain 'f' and resid 6 through 7 removed outlier: 3.511A pdb=" N SER f 7 " --> pdb=" O SER f 22 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'f' and resid 10 through 13 removed outlier: 5.908A pdb=" N LEU f 11 " --> pdb=" O GLU f 109 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN f 41 " --> pdb=" O LEU f 50 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU f 50 " --> pdb=" O GLN f 41 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR f 53 " --> pdb=" O ASN f 57 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN f 57 " --> pdb=" O TYR f 53 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'f' and resid 120 through 122 removed outlier: 3.524A pdb=" N SER f 120 " --> pdb=" O PHE f 139 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL f 137 " --> pdb=" O PHE f 122 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER f 181 " --> pdb=" O CYS f 138 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TYR f 177 " --> pdb=" O ASN f 142 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER f 178 " --> pdb=" O THR f 168 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'f' and resid 148 through 154 removed outlier: 3.772A pdb=" N ASN f 149 " --> pdb=" O THR f 201 " (cutoff:3.500A) 1309 hydrogen bonds defined for protein. 3564 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: 10.32 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11199 1.34 - 1.46: 8444 1.46 - 1.58: 15667 1.58 - 1.70: 0 1.70 - 1.82: 207 Bond restraints: 35517 Sorted by residual: bond pdb=" C THR A 599 " pdb=" N PRO A 600 " ideal model delta sigma weight residual 1.326 1.353 -0.027 1.44e-02 4.82e+03 3.49e+00 bond pdb=" C THR B 599 " pdb=" N PRO B 600 " ideal model delta sigma weight residual 1.326 1.352 -0.026 1.44e-02 4.82e+03 3.19e+00 bond pdb=" N GLN A 14 " pdb=" CA GLN A 14 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.19e+00 bond pdb=" C THR C 599 " pdb=" N PRO C 600 " ideal model delta sigma weight residual 1.326 1.351 -0.025 1.44e-02 4.82e+03 2.99e+00 bond pdb=" N GLN e 1 " pdb=" CA GLN e 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 ... (remaining 35512 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 47153 1.35 - 2.70: 900 2.70 - 4.05: 149 4.05 - 5.40: 144 5.40 - 6.75: 8 Bond angle restraints: 48354 Sorted by residual: angle pdb=" CA VAL e 187 " pdb=" C VAL e 187 " pdb=" N PRO e 188 " ideal model delta sigma weight residual 116.57 120.52 -3.95 9.80e-01 1.04e+00 1.62e+01 angle pdb=" C GLU f 27 " pdb=" N SER f 28 " pdb=" CA SER f 28 " ideal model delta sigma weight residual 121.70 128.45 -6.75 1.80e+00 3.09e-01 1.40e+01 angle pdb=" C GLU d 27 " pdb=" N SER d 28 " pdb=" CA SER d 28 " ideal model delta sigma weight residual 121.70 128.29 -6.59 1.80e+00 3.09e-01 1.34e+01 angle pdb=" C ASP C 215 " pdb=" N LEU C 216 " pdb=" CA LEU C 216 " ideal model delta sigma weight residual 120.83 125.79 -4.96 1.43e+00 4.89e-01 1.20e+01 angle pdb=" C GLU b 27 " pdb=" N SER b 28 " pdb=" CA SER b 28 " ideal model delta sigma weight residual 121.70 127.62 -5.92 1.80e+00 3.09e-01 1.08e+01 ... (remaining 48349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 20668 17.82 - 35.64: 422 35.64 - 53.46: 74 53.46 - 71.29: 14 71.29 - 89.11: 11 Dihedral angle restraints: 21189 sinusoidal: 8196 harmonic: 12993 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 149.62 -56.62 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 143.43 -50.43 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CA ASN C 149 " pdb=" C ASN C 149 " pdb=" N LYS C 150 " pdb=" CA LYS C 150 " ideal model delta harmonic sigma weight residual -180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 21186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3540 0.032 - 0.065: 1317 0.065 - 0.097: 245 0.097 - 0.130: 340 0.130 - 0.162: 30 Chirality restraints: 5472 Sorted by residual: chirality pdb=" CA ILE A 714 " pdb=" N ILE A 714 " pdb=" C ILE A 714 " pdb=" CB ILE A 714 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.57e-01 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 2.59 -0.16 2.00e-01 2.50e+01 6.27e-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 2.59 -0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 5469 not shown) Planarity restraints: 6267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 580 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C GLN B 580 " -0.024 2.00e-02 2.50e+03 pdb=" O GLN B 580 " 0.009 2.00e-02 2.50e+03 pdb=" N THR B 581 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE b 122 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO b 123 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO b 123 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO b 123 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY e 8 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO e 9 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO e 9 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO e 9 " 0.018 5.00e-02 4.00e+02 ... (remaining 6264 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 546 2.67 - 3.22: 32207 3.22 - 3.78: 52117 3.78 - 4.34: 76162 4.34 - 4.90: 124668 Nonbonded interactions: 285700 Sorted by model distance: nonbonded pdb=" OG SER A 968 " pdb=" O GLN C 755 " model vdw 2.106 3.040 nonbonded pdb=" O GLN A 755 " pdb=" OG SER B 968 " model vdw 2.111 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.111 3.040 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.125 3.040 nonbonded pdb=" OG1 THR A 29 " pdb=" OD2 ASP A 215 " model vdw 2.144 3.040 ... (remaining 285695 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'e' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' } 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: 6.180 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: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 36.440 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4680 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35568 Z= 0.147 Angle : 0.551 6.745 48456 Z= 0.302 Chirality : 0.043 0.162 5472 Planarity : 0.003 0.035 6267 Dihedral : 7.923 89.108 12672 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.15 % Allowed : 0.64 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.26 (0.10), residues: 4416 helix: -1.67 (0.14), residues: 699 sheet: -2.04 (0.13), residues: 1216 loop : -2.41 (0.10), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG d 72 TYR 0.013 0.001 TYR B 873 PHE 0.010 0.001 PHE A 497 TRP 0.006 0.001 TRP a 107 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00293 (35517) covalent geometry : angle 0.55134 (48354) SS BOND : bond 0.00142 ( 51) SS BOND : angle 0.62151 ( 102) hydrogen bonds : bond 0.25898 ( 1256) hydrogen bonds : angle 10.54889 ( 3564) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1245 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7280 (p0) cc_final: 0.6098 (t0) REVERT: A 869 MET cc_start: 0.7390 (mtp) cc_final: 0.6741 (mtp) REVERT: A 1004 LEU cc_start: 0.8120 (mt) cc_final: 0.7905 (mt) REVERT: B 900 MET cc_start: 0.6436 (mtp) cc_final: 0.6207 (mtp) REVERT: B 928 ASN cc_start: 0.7190 (m-40) cc_final: 0.6959 (m110) REVERT: C 510 VAL cc_start: 0.5779 (t) cc_final: 0.5549 (t) REVERT: C 573 THR cc_start: 0.6569 (m) cc_final: 0.6244 (m) REVERT: C 644 GLN cc_start: 0.7688 (tp40) cc_final: 0.7480 (tp40) REVERT: C 699 LEU cc_start: 0.8062 (mt) cc_final: 0.7781 (mt) REVERT: C 730 SER cc_start: 0.8460 (p) cc_final: 0.8122 (m) REVERT: C 740 MET cc_start: 0.5429 (mtp) cc_final: 0.4935 (mtm) REVERT: C 753 LEU cc_start: 0.7914 (tp) cc_final: 0.7698 (tt) REVERT: C 777 ASN cc_start: 0.7811 (m-40) cc_final: 0.7609 (m-40) REVERT: e 95 CYS cc_start: 0.2303 (OUTLIER) cc_final: 0.1509 (m) outliers start: 6 outliers final: 2 residues processed: 1250 average time/residue: 0.2095 time to fit residues: 420.6750 Evaluate side-chains 578 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 575 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 144 CYS Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 95 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.4980 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 175 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 925 ASN A 949 GLN A 955 ASN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 360 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 919 ASN B 920 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1083 HIS C 99 ASN C 188 ASN C 856 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS c 86 GLN d 94 GLN e 77 GLN e 102 HIS e 203 HIS ** f 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 216 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.148182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.125292 restraints weight = 108221.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.127359 restraints weight = 55670.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.128660 restraints weight = 33402.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.129477 restraints weight = 22750.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.129918 restraints weight = 17235.993| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 35568 Z= 0.207 Angle : 0.688 16.340 48456 Z= 0.358 Chirality : 0.047 0.209 5472 Planarity : 0.005 0.067 6267 Dihedral : 4.443 44.106 4779 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.82 % Allowed : 10.27 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.11), residues: 4416 helix: 0.05 (0.18), residues: 698 sheet: -1.45 (0.13), residues: 1239 loop : -1.97 (0.11), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 273 TYR 0.026 0.002 TYR B 204 PHE 0.025 0.002 PHE A 888 TRP 0.029 0.002 TRP e 47 HIS 0.009 0.002 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00462 (35517) covalent geometry : angle 0.67985 (48354) SS BOND : bond 0.00748 ( 51) SS BOND : angle 2.38966 ( 102) hydrogen bonds : bond 0.04763 ( 1256) hydrogen bonds : angle 7.29226 ( 3564) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 661 time to evaluate : 1.038 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: b 6 GLN cc_start: 0.2566 (tt0) cc_final: 0.2229 (tt0) REVERT: b 39 TRP cc_start: 0.1710 (m-10) cc_final: 0.1492 (m-10) REVERT: b 58 LEU cc_start: 0.6891 (mt) cc_final: 0.6687 (mt) REVERT: A 540 ASN cc_start: 0.8561 (t0) cc_final: 0.8215 (t0) REVERT: A 695 TYR cc_start: 0.8149 (p90) cc_final: 0.7877 (p90) REVERT: A 1146 ASP cc_start: 0.6614 (m-30) cc_final: 0.6019 (t0) REVERT: B 101 ILE cc_start: 0.8421 (mm) cc_final: 0.8053 (mm) REVERT: B 102 ARG cc_start: 0.6503 (mmm160) cc_final: 0.5512 (mmm160) REVERT: B 140 PHE cc_start: 0.7138 (p90) cc_final: 0.6080 (p90) REVERT: B 240 THR cc_start: 0.5610 (OUTLIER) cc_final: 0.5405 (t) REVERT: B 732 THR cc_start: 0.8620 (m) cc_final: 0.8101 (p) REVERT: B 953 ASN cc_start: 0.8054 (m-40) cc_final: 0.7764 (m-40) REVERT: C 119 ILE cc_start: 0.8435 (mp) cc_final: 0.8038 (mt) REVERT: C 238 PHE cc_start: 0.8085 (p90) cc_final: 0.7844 (p90) REVERT: C 342 PHE cc_start: 0.7511 (m-80) cc_final: 0.6699 (m-80) REVERT: C 765 ARG cc_start: 0.7045 (ttm110) cc_final: 0.6722 (ttm110) REVERT: C 1084 ASP cc_start: 0.5815 (p0) cc_final: 0.5579 (p0) REVERT: c 5 LYS cc_start: 0.6297 (mttt) cc_final: 0.5574 (ttpp) REVERT: c 94 TYR cc_start: 0.3163 (m-80) cc_final: 0.2922 (m-80) REVERT: d 153 LYS cc_start: 0.3229 (ptpt) cc_final: 0.2718 (pttp) REVERT: e 3 GLN cc_start: 0.6227 (tt0) cc_final: 0.5369 (mp10) REVERT: e 142 LEU cc_start: 0.3466 (OUTLIER) cc_final: 0.1602 (mm) REVERT: e 150 PHE cc_start: 0.5240 (t80) cc_final: 0.5005 (t80) REVERT: e 153 PRO cc_start: 0.5966 (Cg_endo) cc_final: 0.5486 (Cg_exo) outliers start: 110 outliers final: 72 residues processed: 737 average time/residue: 0.1944 time to fit residues: 237.4037 Evaluate side-chains 561 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 487 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 920 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain c residue 1 GLN Chi-restraints excluded: chain c residue 82 MET Chi-restraints excluded: chain c residue 144 CYS Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 95 CYS Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 142 LEU Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 149 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 364 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 243 optimal weight: 0.9980 chunk 271 optimal weight: 0.0980 chunk 219 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 363 optimal weight: 0.0670 chunk 233 optimal weight: 2.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 96 ASN A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 606 ASN B 920 GLN B 955 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C1101 HIS e 39 GLN f 41 GLN f 93 GLN f 149 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.147186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.124300 restraints weight = 107605.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.126296 restraints weight = 55330.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.127557 restraints weight = 33198.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.128361 restraints weight = 22585.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.128784 restraints weight = 17243.904| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 35568 Z= 0.154 Angle : 0.606 13.601 48456 Z= 0.315 Chirality : 0.045 0.214 5472 Planarity : 0.005 0.067 6267 Dihedral : 4.417 45.332 4779 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.74 % Allowed : 12.30 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.12), residues: 4416 helix: 0.46 (0.19), residues: 693 sheet: -1.14 (0.14), residues: 1231 loop : -1.80 (0.11), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 403 TYR 0.029 0.002 TYR d 53 PHE 0.026 0.002 PHE C 464 TRP 0.032 0.002 TRP A 886 HIS 0.007 0.001 HIS e 102 Details of bonding type rmsd covalent geometry : bond 0.00348 (35517) covalent geometry : angle 0.59822 (48354) SS BOND : bond 0.00519 ( 51) SS BOND : angle 2.18130 ( 102) hydrogen bonds : bond 0.04243 ( 1256) hydrogen bonds : angle 6.82185 ( 3564) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 562 time to evaluate : 1.388 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: b 6 GLN cc_start: 0.2556 (tt0) cc_final: 0.2229 (tt0) REVERT: b 91 TYR cc_start: 0.0259 (m-80) cc_final: 0.0059 (m-80) REVERT: A 540 ASN cc_start: 0.8543 (t0) cc_final: 0.8191 (t0) REVERT: A 574 ASP cc_start: 0.7512 (p0) cc_final: 0.6350 (t0) REVERT: A 699 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7147 (mt) REVERT: A 1146 ASP cc_start: 0.6511 (m-30) cc_final: 0.6104 (t0) REVERT: B 140 PHE cc_start: 0.6433 (p90) cc_final: 0.5861 (p90) REVERT: B 240 THR cc_start: 0.5252 (OUTLIER) cc_final: 0.5021 (t) REVERT: B 265 TYR cc_start: 0.5027 (p90) cc_final: 0.4805 (p90) REVERT: B 487 ASN cc_start: 0.6039 (t0) cc_final: 0.5831 (m110) REVERT: B 732 THR cc_start: 0.8612 (m) cc_final: 0.8146 (p) REVERT: B 776 LYS cc_start: 0.8498 (tttm) cc_final: 0.7963 (tptm) REVERT: B 900 MET cc_start: 0.6788 (mtp) cc_final: 0.6557 (mtp) REVERT: C 765 ARG cc_start: 0.6952 (ttm110) cc_final: 0.6718 (ttm110) REVERT: C 1084 ASP cc_start: 0.5734 (p0) cc_final: 0.5449 (p0) REVERT: c 5 LYS cc_start: 0.6136 (mttt) cc_final: 0.5370 (ttpp) REVERT: d 107 LYS cc_start: 0.4783 (tptt) cc_final: 0.3823 (mmtp) REVERT: e 3 GLN cc_start: 0.6234 (tt0) cc_final: 0.5361 (mp10) REVERT: e 142 LEU cc_start: 0.3121 (OUTLIER) cc_final: 0.1845 (tp) REVERT: e 153 PRO cc_start: 0.6071 (Cg_endo) cc_final: 0.5688 (Cg_exo) REVERT: f 65 ARG cc_start: 0.2529 (OUTLIER) cc_final: 0.2317 (ptm-80) REVERT: f 74 ASP cc_start: 0.2918 (t70) cc_final: 0.2190 (t0) REVERT: f 146 LYS cc_start: 0.4601 (tttt) cc_final: 0.4312 (tttt) outliers start: 107 outliers final: 62 residues processed: 631 average time/residue: 0.1923 time to fit residues: 200.2738 Evaluate side-chains 536 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 470 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 920 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 82 MET Chi-restraints excluded: chain c residue 144 CYS Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 140 LEU Chi-restraints excluded: chain e residue 20 ILE Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 95 CYS Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 142 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 65 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 96 optimal weight: 5.9990 chunk 371 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 425 optimal weight: 8.9990 chunk 304 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 367 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 378 optimal weight: 0.0470 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 46 GLN A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 914 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 146 HIS B 370 ASN B 606 ASN B 907 ASN B 949 GLN B1005 GLN C 121 ASN C 474 GLN C 762 GLN C 777 ASN C 992 GLN C1101 HIS c 98 ASN e 39 GLN ** f 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 38 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.142739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.120137 restraints weight = 106011.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.122122 restraints weight = 59796.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.122485 restraints weight = 35758.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.122910 restraints weight = 29518.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.123289 restraints weight = 24091.651| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 35568 Z= 0.208 Angle : 0.662 13.549 48456 Z= 0.343 Chirality : 0.046 0.214 5472 Planarity : 0.005 0.067 6267 Dihedral : 4.882 45.254 4778 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.74 % Allowed : 13.02 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.12), residues: 4416 helix: 0.27 (0.18), residues: 725 sheet: -1.13 (0.14), residues: 1256 loop : -1.86 (0.11), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1091 TYR 0.031 0.002 TYR B 495 PHE 0.021 0.002 PHE B 823 TRP 0.038 0.002 TRP A 886 HIS 0.008 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00473 (35517) covalent geometry : angle 0.65619 (48354) SS BOND : bond 0.00575 ( 51) SS BOND : angle 1.95471 ( 102) hydrogen bonds : bond 0.04154 ( 1256) hydrogen bonds : angle 6.62743 ( 3564) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 512 time to evaluate : 1.246 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 107 TRP cc_start: 0.3303 (m100) cc_final: 0.2225 (m100) REVERT: a 109 GLN cc_start: 0.4291 (OUTLIER) cc_final: 0.3628 (tm-30) REVERT: b 129 LEU cc_start: -0.0313 (OUTLIER) cc_final: -0.0716 (mm) REVERT: A 153 MET cc_start: 0.6699 (ptt) cc_final: 0.6331 (mtm) REVERT: A 405 ASP cc_start: 0.7045 (m-30) cc_final: 0.6604 (p0) REVERT: A 540 ASN cc_start: 0.8577 (t0) cc_final: 0.8317 (t0) REVERT: A 900 MET cc_start: 0.7834 (mmm) cc_final: 0.7554 (mmm) REVERT: A 1031 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: A 1037 SER cc_start: 0.8785 (t) cc_final: 0.8496 (m) REVERT: B 140 PHE cc_start: 0.6508 (p90) cc_final: 0.6008 (p90) REVERT: B 549 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7244 (p) REVERT: B 732 THR cc_start: 0.8697 (m) cc_final: 0.8126 (p) REVERT: B 740 MET cc_start: 0.7718 (tpp) cc_final: 0.7384 (tpp) REVERT: B 900 MET cc_start: 0.6914 (mtp) cc_final: 0.6680 (mtp) REVERT: B 966 LEU cc_start: 0.8770 (mt) cc_final: 0.8504 (mt) REVERT: C 417 LYS cc_start: 0.7404 (ttmt) cc_final: 0.7167 (ttmm) REVERT: C 521 PRO cc_start: 0.6286 (Cg_endo) cc_final: 0.6025 (Cg_exo) REVERT: C 730 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8395 (m) REVERT: C 765 ARG cc_start: 0.6909 (ttm110) cc_final: 0.6624 (ttm110) REVERT: C 1084 ASP cc_start: 0.5730 (p0) cc_final: 0.5443 (p0) REVERT: C 1130 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7804 (tp) REVERT: c 5 LYS cc_start: 0.6022 (mttt) cc_final: 0.5221 (ttpp) REVERT: e 3 GLN cc_start: 0.6253 (tt0) cc_final: 0.5205 (mp10) REVERT: f 65 ARG cc_start: 0.2977 (OUTLIER) cc_final: 0.2691 (ptm-80) REVERT: f 74 ASP cc_start: 0.3436 (t70) cc_final: 0.2654 (t0) REVERT: f 111 LYS cc_start: 0.6555 (tttt) cc_final: 0.5902 (mmtp) REVERT: f 146 LYS cc_start: 0.4535 (tttt) cc_final: 0.4281 (tttt) outliers start: 146 outliers final: 104 residues processed: 609 average time/residue: 0.1889 time to fit residues: 192.5600 Evaluate side-chains 551 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 440 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 95 CYS Chi-restraints excluded: chain a residue 109 GLN Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain b residue 50 LEU Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 82 MET Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 144 CYS Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 118 THR Chi-restraints excluded: chain d residue 140 LEU Chi-restraints excluded: chain e residue 20 ILE Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 95 CYS Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 132 SER Chi-restraints excluded: chain e residue 178 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 65 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 391 optimal weight: 5.9990 chunk 344 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 438 optimal weight: 8.9990 chunk 352 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 371 optimal weight: 3.9990 chunk 420 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 46 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 580 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 121 ASN C 125 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 755 GLN C 856 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN c 39 GLN c 60 ASN ** c 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 57 ASN e 3 GLN e 39 GLN ** e 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.139987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.116976 restraints weight = 107096.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.118884 restraints weight = 55647.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.120094 restraints weight = 33897.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.120877 restraints weight = 23402.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.121270 restraints weight = 17963.324| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 35568 Z= 0.242 Angle : 0.695 14.503 48456 Z= 0.364 Chirality : 0.048 0.258 5472 Planarity : 0.005 0.061 6267 Dihedral : 5.344 50.997 4778 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.41 % Allowed : 14.19 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.12), residues: 4416 helix: 0.19 (0.19), residues: 712 sheet: -1.22 (0.14), residues: 1255 loop : -1.91 (0.11), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 355 TYR 0.032 0.002 TYR f 53 PHE 0.022 0.002 PHE C 133 TRP 0.051 0.003 TRP A 886 HIS 0.008 0.002 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00544 (35517) covalent geometry : angle 0.69009 (48354) SS BOND : bond 0.01015 ( 51) SS BOND : angle 1.94011 ( 102) hydrogen bonds : bond 0.04386 ( 1256) hydrogen bonds : angle 6.79647 ( 3564) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 487 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 107 TRP cc_start: 0.3877 (m100) cc_final: 0.2512 (m100) REVERT: a 109 GLN cc_start: 0.4260 (OUTLIER) cc_final: 0.3541 (tm-30) REVERT: b 50 LEU cc_start: 0.2795 (OUTLIER) cc_final: 0.2368 (pt) REVERT: b 129 LEU cc_start: -0.0245 (OUTLIER) cc_final: -0.0567 (mm) REVERT: A 100 ILE cc_start: 0.7910 (mm) cc_final: 0.7518 (mm) REVERT: A 153 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6265 (mtm) REVERT: A 540 ASN cc_start: 0.8572 (t0) cc_final: 0.8347 (t0) REVERT: A 726 ILE cc_start: 0.9356 (mt) cc_final: 0.8920 (pt) REVERT: A 1031 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: A 1037 SER cc_start: 0.9068 (t) cc_final: 0.8636 (m) REVERT: B 140 PHE cc_start: 0.6423 (p90) cc_final: 0.5987 (p90) REVERT: B 549 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7399 (p) REVERT: B 723 THR cc_start: 0.8591 (m) cc_final: 0.8298 (p) REVERT: B 732 THR cc_start: 0.8751 (m) cc_final: 0.8214 (p) REVERT: B 900 MET cc_start: 0.6966 (mtp) cc_final: 0.6729 (mtp) REVERT: C 417 LYS cc_start: 0.7508 (ttmt) cc_final: 0.7092 (mtpp) REVERT: C 456 PHE cc_start: -0.0425 (OUTLIER) cc_final: -0.0694 (p90) REVERT: C 521 PRO cc_start: 0.6272 (Cg_endo) cc_final: 0.6071 (Cg_exo) REVERT: C 730 SER cc_start: 0.8613 (OUTLIER) cc_final: 0.8410 (m) REVERT: C 900 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7469 (ptp) REVERT: C 1084 ASP cc_start: 0.5987 (p0) cc_final: 0.5610 (p0) REVERT: C 1130 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8112 (tp) REVERT: c 5 LYS cc_start: 0.6029 (mttt) cc_final: 0.5275 (ttpp) REVERT: c 209 LYS cc_start: 0.5303 (mmtm) cc_final: 0.3374 (ttmm) REVERT: e 3 GLN cc_start: 0.6237 (tt0) cc_final: 0.5289 (mp10) REVERT: e 45 LEU cc_start: 0.4066 (OUTLIER) cc_final: 0.3848 (tp) REVERT: e 51 MET cc_start: 0.4333 (mmt) cc_final: 0.3976 (mmt) REVERT: f 60 SER cc_start: 0.6778 (OUTLIER) cc_final: 0.6518 (t) REVERT: f 65 ARG cc_start: 0.3325 (OUTLIER) cc_final: 0.2319 (ptm-80) REVERT: f 111 LYS cc_start: 0.6840 (tttt) cc_final: 0.6039 (mmtp) REVERT: f 146 LYS cc_start: 0.4724 (tttt) cc_final: 0.4443 (tttt) REVERT: f 169 ASP cc_start: 0.5465 (p0) cc_final: 0.5180 (p0) REVERT: f 177 TYR cc_start: 0.2748 (OUTLIER) cc_final: 0.2466 (m-10) outliers start: 172 outliers final: 116 residues processed: 609 average time/residue: 0.1922 time to fit residues: 195.1476 Evaluate side-chains 548 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 418 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 95 CYS Chi-restraints excluded: chain a residue 109 GLN Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain b residue 50 LEU Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 1 GLN Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 52 TRP Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 74 ASP Chi-restraints excluded: chain d residue 140 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 45 LEU Chi-restraints excluded: chain e residue 95 CYS Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 132 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 65 ARG Chi-restraints excluded: chain f residue 177 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 258 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 318 optimal weight: 0.7980 chunk 395 optimal weight: 7.9990 chunk 286 optimal weight: 0.9980 chunk 294 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 428 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 907 ASN B1106 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN c 60 ASN c 98 ASN e 3 GLN e 39 GLN ** e 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.141530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.118646 restraints weight = 106163.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.120563 restraints weight = 55060.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.121791 restraints weight = 33479.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.122573 restraints weight = 23012.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.122953 restraints weight = 17638.363| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.6375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35568 Z= 0.153 Angle : 0.604 12.121 48456 Z= 0.316 Chirality : 0.045 0.227 5472 Planarity : 0.005 0.062 6267 Dihedral : 4.929 48.398 4777 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.38 % Allowed : 15.96 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.12), residues: 4416 helix: 0.41 (0.19), residues: 696 sheet: -1.14 (0.14), residues: 1235 loop : -1.80 (0.11), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 357 TYR 0.026 0.002 TYR A 904 PHE 0.021 0.002 PHE b 143 TRP 0.055 0.002 TRP A 886 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00349 (35517) covalent geometry : angle 0.60045 (48354) SS BOND : bond 0.00481 ( 51) SS BOND : angle 1.55822 ( 102) hydrogen bonds : bond 0.03900 ( 1256) hydrogen bonds : angle 6.49420 ( 3564) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 466 time to evaluate : 1.224 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 107 TRP cc_start: 0.3539 (m100) cc_final: 0.2423 (m100) REVERT: a 109 GLN cc_start: 0.4140 (OUTLIER) cc_final: 0.3451 (tm-30) REVERT: b 50 LEU cc_start: 0.2846 (OUTLIER) cc_final: 0.2372 (pt) REVERT: b 129 LEU cc_start: -0.0327 (OUTLIER) cc_final: -0.0648 (mm) REVERT: A 153 MET cc_start: 0.6831 (ptt) cc_final: 0.6262 (mtm) REVERT: A 574 ASP cc_start: 0.7546 (p0) cc_final: 0.6459 (t0) REVERT: A 904 TYR cc_start: 0.5638 (t80) cc_final: 0.5377 (t80) REVERT: A 1031 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: A 1037 SER cc_start: 0.9077 (t) cc_final: 0.8605 (m) REVERT: A 1146 ASP cc_start: 0.6952 (m-30) cc_final: 0.6159 (t0) REVERT: B 102 ARG cc_start: 0.6948 (mmm160) cc_final: 0.6209 (mmm160) REVERT: B 140 PHE cc_start: 0.6311 (p90) cc_final: 0.6031 (p90) REVERT: B 360 ASN cc_start: 0.6250 (m-40) cc_final: 0.5563 (p0) REVERT: B 423 TYR cc_start: 0.6003 (t80) cc_final: 0.5794 (t80) REVERT: B 549 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7327 (p) REVERT: B 732 THR cc_start: 0.8702 (m) cc_final: 0.8217 (p) REVERT: B 900 MET cc_start: 0.6954 (mtp) cc_final: 0.6680 (mtp) REVERT: C 417 LYS cc_start: 0.7496 (ttmt) cc_final: 0.7184 (ttmm) REVERT: C 464 PHE cc_start: 0.5754 (m-80) cc_final: 0.5436 (t80) REVERT: C 730 SER cc_start: 0.8607 (p) cc_final: 0.8394 (m) REVERT: C 765 ARG cc_start: 0.7030 (ttm110) cc_final: 0.6704 (ttm110) REVERT: C 900 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7354 (ptp) REVERT: C 1084 ASP cc_start: 0.5956 (p0) cc_final: 0.5627 (p0) REVERT: C 1130 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8063 (tp) REVERT: c 209 LYS cc_start: 0.5277 (mmtm) cc_final: 0.3396 (ttmm) REVERT: d 110 ILE cc_start: 0.5439 (mt) cc_final: 0.5001 (mm) REVERT: e 3 GLN cc_start: 0.6217 (tt0) cc_final: 0.5218 (mp10) REVERT: e 51 MET cc_start: 0.4038 (mmt) cc_final: 0.3718 (mmm) REVERT: e 153 PRO cc_start: 0.6156 (Cg_endo) cc_final: 0.5721 (Cg_exo) REVERT: f 146 LYS cc_start: 0.5033 (OUTLIER) cc_final: 0.4729 (tttt) REVERT: f 169 ASP cc_start: 0.5726 (p0) cc_final: 0.5479 (p0) outliers start: 132 outliers final: 94 residues processed: 552 average time/residue: 0.1930 time to fit residues: 177.7385 Evaluate side-chains 523 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 421 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 109 GLN Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain b residue 50 LEU Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain c residue 1 GLN Chi-restraints excluded: chain c residue 52 TRP Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 14 SER Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 140 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 95 CYS Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 132 SER Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 146 LYS Chi-restraints excluded: chain f residue 197 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 309 optimal weight: 0.0970 chunk 323 optimal weight: 0.9990 chunk 436 optimal weight: 7.9990 chunk 342 optimal weight: 0.9980 chunk 393 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 326 optimal weight: 0.9990 chunk 407 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 907 ASN B 949 GLN B 953 ASN B 955 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN c 60 ASN d 42 GLN d 57 ASN e 39 GLN ** e 203 HIS ** 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 = 0.4245 r_free = 0.4245 target = 0.142013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.119134 restraints weight = 106682.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.121067 restraints weight = 55290.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.122292 restraints weight = 33540.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.123043 restraints weight = 23078.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.123566 restraints weight = 17750.151| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.6495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 35568 Z= 0.137 Angle : 0.586 11.139 48456 Z= 0.306 Chirality : 0.044 0.217 5472 Planarity : 0.004 0.062 6267 Dihedral : 4.753 47.776 4777 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.41 % Allowed : 16.35 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.12), residues: 4416 helix: 0.57 (0.19), residues: 681 sheet: -1.06 (0.15), residues: 1227 loop : -1.73 (0.11), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 357 TYR 0.031 0.002 TYR d 91 PHE 0.030 0.002 PHE B 374 TRP 0.059 0.002 TRP A 886 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00318 (35517) covalent geometry : angle 0.58274 (48354) SS BOND : bond 0.00456 ( 51) SS BOND : angle 1.51872 ( 102) hydrogen bonds : bond 0.03779 ( 1256) hydrogen bonds : angle 6.29659 ( 3564) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 455 time to evaluate : 1.099 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 107 TRP cc_start: 0.3550 (m100) cc_final: 0.2504 (m100) REVERT: a 109 GLN cc_start: 0.4031 (OUTLIER) cc_final: 0.3376 (tm-30) REVERT: b 50 LEU cc_start: 0.2712 (OUTLIER) cc_final: 0.2256 (pt) REVERT: b 129 LEU cc_start: -0.0355 (OUTLIER) cc_final: -0.0671 (mm) REVERT: A 45 SER cc_start: 0.8013 (t) cc_final: 0.7638 (p) REVERT: A 100 ILE cc_start: 0.7893 (mm) cc_final: 0.7564 (mm) REVERT: A 153 MET cc_start: 0.6750 (ptt) cc_final: 0.6242 (mtm) REVERT: A 904 TYR cc_start: 0.5599 (t80) cc_final: 0.5393 (t80) REVERT: A 1031 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: A 1037 SER cc_start: 0.9069 (t) cc_final: 0.8540 (m) REVERT: A 1110 TYR cc_start: 0.6625 (t80) cc_final: 0.6245 (t80) REVERT: A 1146 ASP cc_start: 0.6735 (m-30) cc_final: 0.6082 (t0) REVERT: B 102 ARG cc_start: 0.6907 (mmm160) cc_final: 0.6153 (mmm160) REVERT: B 140 PHE cc_start: 0.6250 (p90) cc_final: 0.6048 (p90) REVERT: B 200 TYR cc_start: 0.5016 (OUTLIER) cc_final: 0.4414 (m-80) REVERT: B 360 ASN cc_start: 0.6293 (m-40) cc_final: 0.6026 (p0) REVERT: B 423 TYR cc_start: 0.6120 (t80) cc_final: 0.5903 (t80) REVERT: B 549 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7334 (p) REVERT: B 732 THR cc_start: 0.8680 (m) cc_final: 0.8198 (p) REVERT: C 417 LYS cc_start: 0.7447 (ttmt) cc_final: 0.7153 (ttmm) REVERT: C 464 PHE cc_start: 0.5777 (m-80) cc_final: 0.5552 (t80) REVERT: C 730 SER cc_start: 0.8598 (OUTLIER) cc_final: 0.8381 (m) REVERT: C 753 LEU cc_start: 0.9028 (tp) cc_final: 0.8822 (tt) REVERT: C 756 TYR cc_start: 0.7169 (m-80) cc_final: 0.6729 (m-80) REVERT: C 765 ARG cc_start: 0.7011 (ttm110) cc_final: 0.6713 (ttm110) REVERT: C 900 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.7148 (ptp) REVERT: C 1084 ASP cc_start: 0.5859 (p0) cc_final: 0.5477 (p0) REVERT: c 209 LYS cc_start: 0.5207 (mmtm) cc_final: 0.3328 (ttmm) REVERT: d 110 ILE cc_start: 0.5400 (mt) cc_final: 0.4939 (mm) REVERT: e 3 GLN cc_start: 0.6232 (tt0) cc_final: 0.5244 (mp10) REVERT: e 153 PRO cc_start: 0.6415 (Cg_endo) cc_final: 0.6025 (Cg_exo) REVERT: f 6 GLN cc_start: 0.4228 (OUTLIER) cc_final: 0.3905 (pp30) REVERT: f 146 LYS cc_start: 0.5035 (tttt) cc_final: 0.4812 (tttt) REVERT: f 169 ASP cc_start: 0.5693 (p0) cc_final: 0.5443 (p0) REVERT: f 177 TYR cc_start: 0.2823 (OUTLIER) cc_final: 0.2522 (m-10) outliers start: 133 outliers final: 99 residues processed: 547 average time/residue: 0.1905 time to fit residues: 172.8558 Evaluate side-chains 524 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 415 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 109 GLN Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain b residue 50 LEU Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain c residue 1 GLN Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 52 TRP Chi-restraints excluded: chain c residue 82 MET Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 140 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 95 CYS Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 132 SER Chi-restraints excluded: chain e residue 174 LEU Chi-restraints excluded: chain f residue 6 GLN Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 177 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 9 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 339 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 392 optimal weight: 0.8980 chunk 228 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 188 ASN B 501 ASN B 690 GLN B 907 ASN B 935 GLN B 955 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN c 86 GLN e 3 GLN ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 HIS ** 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 = 0.4223 r_free = 0.4223 target = 0.140608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.117827 restraints weight = 106961.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.119716 restraints weight = 55521.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.120901 restraints weight = 33786.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.121692 restraints weight = 23338.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.122121 restraints weight = 17925.550| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35568 Z= 0.171 Angle : 0.612 12.251 48456 Z= 0.321 Chirality : 0.045 0.247 5472 Planarity : 0.005 0.064 6267 Dihedral : 4.921 50.418 4777 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.64 % Allowed : 16.68 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.12), residues: 4416 helix: 0.61 (0.19), residues: 679 sheet: -1.07 (0.15), residues: 1219 loop : -1.72 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 403 TYR 0.026 0.002 TYR d 91 PHE 0.021 0.002 PHE B 192 TRP 0.064 0.002 TRP A 886 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00393 (35517) covalent geometry : angle 0.60869 (48354) SS BOND : bond 0.00449 ( 51) SS BOND : angle 1.59486 ( 102) hydrogen bonds : bond 0.03847 ( 1256) hydrogen bonds : angle 6.29744 ( 3564) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 435 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 107 TRP cc_start: 0.3709 (m100) cc_final: 0.2672 (m100) REVERT: a 109 GLN cc_start: 0.4181 (OUTLIER) cc_final: 0.3485 (tm-30) REVERT: a 139 MET cc_start: 0.3898 (tpp) cc_final: 0.3577 (ttt) REVERT: b 100 PHE cc_start: 0.3136 (m-80) cc_final: 0.2865 (m-10) REVERT: b 129 LEU cc_start: -0.0323 (OUTLIER) cc_final: -0.0645 (mm) REVERT: A 153 MET cc_start: 0.6689 (ptt) cc_final: 0.6129 (mtm) REVERT: A 1031 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: A 1037 SER cc_start: 0.9075 (t) cc_final: 0.8563 (m) REVERT: A 1110 TYR cc_start: 0.6816 (t80) cc_final: 0.6545 (t80) REVERT: A 1146 ASP cc_start: 0.6843 (m-30) cc_final: 0.6090 (t0) REVERT: B 140 PHE cc_start: 0.6389 (p90) cc_final: 0.6173 (p90) REVERT: B 200 TYR cc_start: 0.5090 (OUTLIER) cc_final: 0.4432 (m-80) REVERT: B 549 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7416 (p) REVERT: B 732 THR cc_start: 0.8692 (m) cc_final: 0.8220 (p) REVERT: C 417 LYS cc_start: 0.7439 (ttmt) cc_final: 0.7099 (ttmm) REVERT: C 456 PHE cc_start: -0.0495 (OUTLIER) cc_final: -0.0853 (p90) REVERT: C 527 PRO cc_start: 0.7296 (Cg_endo) cc_final: 0.7019 (Cg_exo) REVERT: C 730 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8449 (m) REVERT: C 753 LEU cc_start: 0.9063 (tp) cc_final: 0.8796 (tt) REVERT: C 756 TYR cc_start: 0.7229 (m-80) cc_final: 0.6865 (m-80) REVERT: C 1084 ASP cc_start: 0.5943 (p0) cc_final: 0.5591 (p0) REVERT: c 86 GLN cc_start: 0.6984 (mp-120) cc_final: 0.6735 (mp10) REVERT: c 209 LYS cc_start: 0.5202 (mmtm) cc_final: 0.3333 (ttmm) REVERT: d 110 ILE cc_start: 0.5345 (mt) cc_final: 0.4901 (mm) REVERT: e 3 GLN cc_start: 0.6161 (tt0) cc_final: 0.5291 (mp10) REVERT: e 153 PRO cc_start: 0.6179 (Cg_endo) cc_final: 0.5744 (Cg_exo) REVERT: f 6 GLN cc_start: 0.3836 (OUTLIER) cc_final: 0.3633 (pp30) REVERT: f 146 LYS cc_start: 0.5137 (OUTLIER) cc_final: 0.4897 (tttt) REVERT: f 169 ASP cc_start: 0.5563 (p0) cc_final: 0.5340 (p0) REVERT: f 177 TYR cc_start: 0.2660 (OUTLIER) cc_final: 0.2402 (m-10) outliers start: 142 outliers final: 117 residues processed: 533 average time/residue: 0.1850 time to fit residues: 166.3769 Evaluate side-chains 532 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 405 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 95 CYS Chi-restraints excluded: chain a residue 109 GLN Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain c residue 1 GLN Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 52 TRP Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 74 ASP Chi-restraints excluded: chain d residue 140 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 82 MET Chi-restraints excluded: chain e residue 95 CYS Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 132 SER Chi-restraints excluded: chain e residue 174 LEU Chi-restraints excluded: chain f residue 6 GLN Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 146 LYS Chi-restraints excluded: chain f residue 177 TYR Chi-restraints excluded: chain f residue 197 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 5 optimal weight: 0.8980 chunk 289 optimal weight: 0.9990 chunk 116 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 407 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 376 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 349 optimal weight: 0.9990 chunk 321 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 239 GLN B 613 GLN B 690 GLN B 907 ASN B 955 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN e 39 GLN ** e 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.141576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.118826 restraints weight = 106381.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.120716 restraints weight = 55347.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.121949 restraints weight = 33607.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.122710 restraints weight = 23174.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.123164 restraints weight = 17812.659| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.6880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35568 Z= 0.137 Angle : 0.598 11.467 48456 Z= 0.313 Chirality : 0.044 0.219 5472 Planarity : 0.005 0.061 6267 Dihedral : 4.810 50.117 4777 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.10 % Allowed : 17.68 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.12), residues: 4416 helix: 0.65 (0.19), residues: 685 sheet: -1.01 (0.15), residues: 1236 loop : -1.74 (0.12), residues: 2495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 403 TYR 0.034 0.002 TYR A 904 PHE 0.034 0.002 PHE C1109 TRP 0.079 0.002 TRP A 886 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00317 (35517) covalent geometry : angle 0.59273 (48354) SS BOND : bond 0.00426 ( 51) SS BOND : angle 1.82531 ( 102) hydrogen bonds : bond 0.03699 ( 1256) hydrogen bonds : angle 6.18644 ( 3564) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 439 time to evaluate : 1.259 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 107 TRP cc_start: 0.3661 (m100) cc_final: 0.2708 (m100) REVERT: a 109 GLN cc_start: 0.4450 (OUTLIER) cc_final: 0.3961 (tm-30) REVERT: a 139 MET cc_start: 0.3918 (tpp) cc_final: 0.3646 (ttp) REVERT: b 100 PHE cc_start: 0.3138 (m-80) cc_final: 0.2854 (m-10) REVERT: b 129 LEU cc_start: -0.0103 (OUTLIER) cc_final: -0.0445 (mm) REVERT: A 45 SER cc_start: 0.7968 (t) cc_final: 0.7562 (p) REVERT: A 153 MET cc_start: 0.6565 (ptt) cc_final: 0.5972 (mtm) REVERT: A 1031 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: A 1037 SER cc_start: 0.9030 (t) cc_final: 0.8618 (m) REVERT: A 1110 TYR cc_start: 0.6841 (t80) cc_final: 0.6550 (t80) REVERT: A 1146 ASP cc_start: 0.6779 (m-30) cc_final: 0.6124 (t0) REVERT: B 102 ARG cc_start: 0.7009 (mmm160) cc_final: 0.6327 (mmm160) REVERT: B 200 TYR cc_start: 0.5094 (OUTLIER) cc_final: 0.4558 (m-80) REVERT: B 492 LEU cc_start: 0.2327 (mp) cc_final: 0.1733 (mp) REVERT: B 549 THR cc_start: 0.7863 (OUTLIER) cc_final: 0.7351 (p) REVERT: B 732 THR cc_start: 0.8687 (m) cc_final: 0.8227 (p) REVERT: C 119 ILE cc_start: 0.8603 (mp) cc_final: 0.8267 (mt) REVERT: C 417 LYS cc_start: 0.7454 (ttmt) cc_final: 0.7091 (ttmm) REVERT: C 464 PHE cc_start: 0.6035 (OUTLIER) cc_final: 0.5811 (t80) REVERT: C 527 PRO cc_start: 0.7107 (Cg_endo) cc_final: 0.6800 (Cg_exo) REVERT: C 730 SER cc_start: 0.8633 (p) cc_final: 0.8423 (m) REVERT: C 756 TYR cc_start: 0.7147 (m-80) cc_final: 0.6634 (m-80) REVERT: C 765 ARG cc_start: 0.7029 (ttm110) cc_final: 0.6779 (ttm110) REVERT: C 1084 ASP cc_start: 0.5877 (p0) cc_final: 0.5432 (p0) REVERT: C 1130 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8225 (tp) REVERT: c 86 GLN cc_start: 0.6950 (mp-120) cc_final: 0.6676 (mp10) REVERT: c 209 LYS cc_start: 0.5087 (mmtm) cc_final: 0.3225 (ttmm) REVERT: d 110 ILE cc_start: 0.5330 (mt) cc_final: 0.4867 (mm) REVERT: e 3 GLN cc_start: 0.6178 (tt0) cc_final: 0.5306 (mp10) REVERT: e 86 GLN cc_start: 0.5093 (tp40) cc_final: 0.4549 (tt0) REVERT: e 153 PRO cc_start: 0.6130 (Cg_endo) cc_final: 0.5705 (Cg_exo) REVERT: f 146 LYS cc_start: 0.5071 (tttt) cc_final: 0.4694 (tttt) outliers start: 121 outliers final: 101 residues processed: 526 average time/residue: 0.1856 time to fit residues: 163.7036 Evaluate side-chains 516 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 408 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 109 GLN Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain c residue 1 GLN Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 52 TRP Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 74 ASP Chi-restraints excluded: chain d residue 140 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 82 MET Chi-restraints excluded: chain e residue 95 CYS Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 132 SER Chi-restraints excluded: chain e residue 174 LEU Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 293 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 400 optimal weight: 4.9990 chunk 357 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 273 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 39 GLN a 168 HIS A 481 ASN A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 907 ASN B1005 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN c 168 HIS ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.139647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.117068 restraints weight = 106954.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.118933 restraints weight = 56080.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.120119 restraints weight = 34378.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.120886 restraints weight = 23747.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.121274 restraints weight = 18255.066| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.7166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 35568 Z= 0.200 Angle : 0.649 12.598 48456 Z= 0.341 Chirality : 0.046 0.271 5472 Planarity : 0.005 0.066 6267 Dihedral : 5.091 53.329 4777 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.33 % Allowed : 17.55 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.12), residues: 4416 helix: 0.47 (0.19), residues: 693 sheet: -1.09 (0.14), residues: 1238 loop : -1.80 (0.12), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 357 TYR 0.046 0.002 TYR A 904 PHE 0.026 0.002 PHE C1109 TRP 0.096 0.003 TRP A 886 HIS 0.008 0.001 HIS a 35 Details of bonding type rmsd covalent geometry : bond 0.00459 (35517) covalent geometry : angle 0.64373 (48354) SS BOND : bond 0.00416 ( 51) SS BOND : angle 1.83309 ( 102) hydrogen bonds : bond 0.03936 ( 1256) hydrogen bonds : angle 6.33136 ( 3564) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 421 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 3 GLN cc_start: 0.4331 (tt0) cc_final: 0.3684 (mp10) REVERT: a 107 TRP cc_start: 0.3755 (m100) cc_final: 0.2785 (m100) REVERT: a 109 GLN cc_start: 0.4628 (OUTLIER) cc_final: 0.4096 (tm-30) REVERT: b 100 PHE cc_start: 0.3179 (m-80) cc_final: 0.2875 (m-10) REVERT: b 129 LEU cc_start: -0.0206 (OUTLIER) cc_final: -0.0524 (mm) REVERT: A 153 MET cc_start: 0.6677 (ptt) cc_final: 0.6074 (mtm) REVERT: A 1031 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: A 1037 SER cc_start: 0.9028 (t) cc_final: 0.8627 (m) REVERT: A 1110 TYR cc_start: 0.7042 (t80) cc_final: 0.6762 (t80) REVERT: A 1146 ASP cc_start: 0.6893 (m-30) cc_final: 0.6258 (t0) REVERT: B 200 TYR cc_start: 0.5315 (OUTLIER) cc_final: 0.4617 (m-80) REVERT: B 549 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7427 (p) REVERT: B 732 THR cc_start: 0.8737 (m) cc_final: 0.8268 (p) REVERT: B 990 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7644 (tt0) REVERT: C 119 ILE cc_start: 0.8632 (mp) cc_final: 0.8310 (mt) REVERT: C 417 LYS cc_start: 0.7456 (ttmt) cc_final: 0.7121 (ttmm) REVERT: C 527 PRO cc_start: 0.7215 (Cg_endo) cc_final: 0.6897 (Cg_exo) REVERT: C 756 TYR cc_start: 0.7192 (m-80) cc_final: 0.6862 (m-80) REVERT: C 1084 ASP cc_start: 0.6020 (p0) cc_final: 0.5630 (p0) REVERT: C 1130 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8274 (tp) REVERT: c 86 GLN cc_start: 0.6979 (mp-120) cc_final: 0.6704 (mp10) REVERT: c 209 LYS cc_start: 0.5135 (mmtm) cc_final: 0.3275 (ttmm) REVERT: d 110 ILE cc_start: 0.5349 (mt) cc_final: 0.4890 (mm) REVERT: e 3 GLN cc_start: 0.6188 (tt0) cc_final: 0.5321 (mp10) REVERT: e 153 PRO cc_start: 0.6139 (Cg_endo) cc_final: 0.5712 (Cg_exo) REVERT: f 74 ASP cc_start: 0.2809 (t70) cc_final: 0.2176 (t0) REVERT: f 111 LYS cc_start: 0.6993 (tttt) cc_final: 0.6039 (mtpp) REVERT: f 146 LYS cc_start: 0.4989 (tttt) cc_final: 0.4609 (tttt) outliers start: 130 outliers final: 111 residues processed: 515 average time/residue: 0.1823 time to fit residues: 159.6687 Evaluate side-chains 518 residues out of total 3903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 401 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 109 GLN Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain c residue 1 GLN Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 52 TRP Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 140 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain e residue 95 CYS Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 174 LEU Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 185 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 334 optimal weight: 0.9980 chunk 253 optimal weight: 7.9990 chunk 227 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 131 optimal weight: 0.0010 chunk 69 optimal weight: 0.3980 chunk 352 optimal weight: 0.8980 chunk 393 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B1005 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.139786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.117293 restraints weight = 105942.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.119148 restraints weight = 55363.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.120320 restraints weight = 33908.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.121000 restraints weight = 23434.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.121523 restraints weight = 18259.986| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.7186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.320 35568 Z= 0.247 Angle : 0.823 59.167 48456 Z= 0.469 Chirality : 0.046 0.572 5472 Planarity : 0.005 0.129 6267 Dihedral : 5.101 53.286 4777 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.33 % Allowed : 17.65 % Favored : 79.02 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.12), residues: 4416 helix: 0.47 (0.19), residues: 693 sheet: -1.11 (0.14), residues: 1240 loop : -1.80 (0.12), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG C 355 TYR 0.041 0.002 TYR c 32 PHE 0.046 0.002 PHE c 27 TRP 0.082 0.002 TRP A 886 HIS 0.007 0.001 HIS a 35 Details of bonding type rmsd covalent geometry : bond 0.00582 (35517) covalent geometry : angle 0.81183 (48354) SS BOND : bond 0.00786 ( 51) SS BOND : angle 3.11665 ( 102) hydrogen bonds : bond 0.03934 ( 1256) hydrogen bonds : angle 6.33206 ( 3564) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6942.60 seconds wall clock time: 120 minutes 30.68 seconds (7230.68 seconds total)