Starting phenix.real_space_refine on Sat Feb 7 16:50:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z6w_39806/02_2026/8z6w_39806.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z6w_39806/02_2026/8z6w_39806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z6w_39806/02_2026/8z6w_39806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z6w_39806/02_2026/8z6w_39806.map" model { file = "/net/cci-nas-00/data/ceres_data/8z6w_39806/02_2026/8z6w_39806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z6w_39806/02_2026/8z6w_39806.cif" } resolution = 3.04 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= 0.000 sd= 0.042 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 22260 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 131 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34950 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 8502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8502 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 60, 'TRANS': 1026} Chain breaks: 6 Chain: "A" Number of atoms: 8502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8502 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 60, 'TRANS': 1026} Chain breaks: 6 Chain: "J" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1502 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "G" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1646 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "K" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1502 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "H" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1646 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "L" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1502 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "I" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1646 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "C" Number of atoms: 8502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8502 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 60, 'TRANS': 1026} Chain breaks: 6 Time building chain proxies: 8.02, per 1000 atoms: 0.23 Number of scatterers: 34950 At special positions: 0 Unit cell: (164.22, 146.37, 224.91, 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 22260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS B 132 " - 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=2.04 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=2.02 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 B 840 " - pdb=" SG CYS B 851 " 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 A 132 " - 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 A 840 " - pdb=" SG CYS A 851 " 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 J 23 " - pdb=" SG CYS J 104 " distance=2.03 Simple disulfide: pdb=" SG CYS J 155 " - pdb=" SG CYS J 214 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 104 " distance=2.03 Simple disulfide: pdb=" SG CYS G 155 " - pdb=" SG CYS G 211 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 104 " distance=2.03 Simple disulfide: pdb=" SG CYS K 155 " - pdb=" SG CYS K 214 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 155 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - 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=2.04 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=2.04 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 C 840 " - pdb=" SG CYS C 851 " 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 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: 2.83 Conformation dependent library (CDL) restraints added in 1.5 seconds 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8406 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 66 sheets defined 19.2% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.022A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.965A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.285A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 753 through 757 removed outlier: 3.538A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.660A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 840 removed outlier: 3.644A pdb=" N CYS B 840 " --> pdb=" O TYR B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 removed outlier: 4.047A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.834A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.572A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.356A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.623A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.519A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.825A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.933A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.236A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 752 through 757 removed outlier: 3.603A pdb=" N GLY A 757 " --> pdb=" O LEU A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.529A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 840 removed outlier: 3.577A pdb=" N CYS A 840 " --> pdb=" O TYR A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.964A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.794A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.053A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.654A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 99 removed outlier: 3.765A pdb=" N GLU J 99 " --> pdb=" O ALA J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 148 Processing helix chain 'J' and resid 202 through 207 Processing helix chain 'G' and resid 95 through 99 removed outlier: 4.167A pdb=" N THR G 99 " --> pdb=" O ALA G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.946A pdb=" N LEU G 204 " --> pdb=" O SER G 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 99 removed outlier: 3.839A pdb=" N GLU K 99 " --> pdb=" O ALA K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 148 Processing helix chain 'K' and resid 202 through 207 Processing helix chain 'H' and resid 95 through 99 removed outlier: 4.173A pdb=" N THR H 99 " --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 204 removed outlier: 3.961A pdb=" N LEU H 204 " --> pdb=" O SER H 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 99 removed outlier: 3.835A pdb=" N GLU L 99 " --> pdb=" O ALA L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 148 Processing helix chain 'L' and resid 202 through 207 Processing helix chain 'I' and resid 95 through 99 removed outlier: 4.133A pdb=" N THR I 99 " --> pdb=" O ALA I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 204 removed outlier: 3.937A pdb=" N LEU I 204 " --> pdb=" O SER I 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.880A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.919A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.275A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.527A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.676A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 840 removed outlier: 3.629A pdb=" N CYS C 840 " --> pdb=" O TYR C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 removed outlier: 4.024A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.805A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.589A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.327A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) 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: 3.646A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.625A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 32 removed outlier: 3.531A pdb=" N SER B 32 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER B 61 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN B 62 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR B 269 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 95 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 43 through 44 removed outlier: 3.540A pdb=" N ARG A 567 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 541 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 327 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 56 removed outlier: 3.938A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.619A pdb=" N GLY B 104 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG B 103 " --> pdb=" O ASN B 122 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 168 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 317 through 320 removed outlier: 4.283A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 326 through 328 removed outlier: 6.503A pdb=" N VAL B 327 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE B 565 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.786A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 435 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.582A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.821A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AB2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.718A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.718A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.284A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AB6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'A' and resid 27 through 32 removed outlier: 3.528A pdb=" N SER A 32 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER A 61 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ASN A 62 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR A 269 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 95 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.892A pdb=" N ARG C 567 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 327 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 49 through 56 removed outlier: 3.895A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.632A pdb=" N GLY A 104 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ARG A 103 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 168 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 317 through 320 removed outlier: 4.317A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.743A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 435 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.644A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.792A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.736A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.736A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.301A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AD1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'J' and resid 9 through 12 removed outlier: 3.722A pdb=" N THR J 125 " --> pdb=" O ALA J 11 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLN J 43 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU J 52 " --> pdb=" O GLN J 43 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 9 through 12 removed outlier: 3.722A pdb=" N THR J 125 " --> pdb=" O ALA J 11 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 19 through 24 removed outlier: 3.545A pdb=" N VAL J 19 " --> pdb=" O ILE J 91 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 138 through 139 removed outlier: 3.919A pdb=" N VAL J 154 " --> pdb=" O PHE J 139 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP J 159 " --> pdb=" O TYR J 193 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TYR J 193 " --> pdb=" O ASP J 159 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER J 196 " --> pdb=" O THR J 183 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR J 183 " --> pdb=" O SER J 196 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU J 181 " --> pdb=" O TYR J 198 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 168 through 170 removed outlier: 3.731A pdb=" N LYS J 170 " --> pdb=" O SER J 213 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER J 213 " --> pdb=" O LYS J 170 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.538A pdb=" N LEU G 19 " --> pdb=" O TRP G 91 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 66 through 67 removed outlier: 7.147A pdb=" N TRP G 41 " --> pdb=" O MET G 53 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE G 55 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE G 39 " --> pdb=" O ILE G 55 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 135 through 139 removed outlier: 3.576A pdb=" N LYS G 158 " --> pdb=" O SER G 135 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS G 155 " --> pdb=" O SER G 195 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER G 195 " --> pdb=" O CYS G 155 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP G 159 " --> pdb=" O TYR G 191 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR G 191 " --> pdb=" O ASP G 159 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER G 194 " --> pdb=" O PHE G 181 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL G 196 " --> pdb=" O HIS G 179 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 166 through 169 removed outlier: 3.673A pdb=" N THR G 166 " --> pdb=" O ASN G 214 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS G 215 " --> pdb=" O THR G 220 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.487A pdb=" N GLN K 43 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU K 52 " --> pdb=" O GLN K 43 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 9 through 13 Processing sheet with id=AE4, first strand: chain 'K' and resid 19 through 24 removed outlier: 3.566A pdb=" N VAL K 19 " --> pdb=" O ILE K 91 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 135 through 139 removed outlier: 3.688A pdb=" N SER K 158 " --> pdb=" O SER K 135 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL K 154 " --> pdb=" O PHE K 139 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP K 159 " --> pdb=" O TYR K 193 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TYR K 193 " --> pdb=" O ASP K 159 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER K 196 " --> pdb=" O THR K 183 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR K 183 " --> pdb=" O SER K 196 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU K 181 " --> pdb=" O TYR K 198 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 168 through 170 removed outlier: 3.703A pdb=" N LYS K 170 " --> pdb=" O SER K 213 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER K 213 " --> pdb=" O LYS K 170 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.545A pdb=" N THR H 77 " --> pdb=" O HIS H 90 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.578A pdb=" N ILE H 39 " --> pdb=" O ILE H 55 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE H 55 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TRP H 41 " --> pdb=" O MET H 53 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 135 through 139 removed outlier: 3.573A pdb=" N LYS H 158 " --> pdb=" O SER H 135 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS H 155 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER H 195 " --> pdb=" O CYS H 155 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP H 159 " --> pdb=" O TYR H 191 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER H 194 " --> pdb=" O PHE H 181 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL H 196 " --> pdb=" O HIS H 179 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 166 through 169 removed outlier: 3.673A pdb=" N THR H 166 " --> pdb=" O ASN H 214 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS H 215 " --> pdb=" O THR H 220 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.529A pdb=" N THR L 122 " --> pdb=" O TYR L 102 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN L 43 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU L 52 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.529A pdb=" N THR L 122 " --> pdb=" O TYR L 102 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.516A pdb=" N VAL L 19 " --> pdb=" O ILE L 91 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 135 through 139 removed outlier: 3.613A pdb=" N SER L 158 " --> pdb=" O SER L 135 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL L 154 " --> pdb=" O PHE L 139 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP L 159 " --> pdb=" O TYR L 193 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR L 193 " --> pdb=" O ASP L 159 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER L 196 " --> pdb=" O THR L 183 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR L 183 " --> pdb=" O SER L 196 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU L 181 " --> pdb=" O TYR L 198 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 168 through 170 removed outlier: 3.680A pdb=" N LYS L 170 " --> pdb=" O SER L 213 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER L 213 " --> pdb=" O LYS L 170 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.525A pdb=" N LEU I 19 " --> pdb=" O TRP I 91 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR I 77 " --> pdb=" O HIS I 90 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.624A pdb=" N ILE I 39 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE I 55 " --> pdb=" O ILE I 39 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TRP I 41 " --> pdb=" O MET I 53 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 135 through 139 removed outlier: 3.507A pdb=" N LYS I 158 " --> pdb=" O SER I 135 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS I 155 " --> pdb=" O SER I 195 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER I 195 " --> pdb=" O CYS I 155 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP I 159 " --> pdb=" O TYR I 191 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER I 194 " --> pdb=" O PHE I 181 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL I 196 " --> pdb=" O HIS I 179 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 166 through 169 removed outlier: 3.666A pdb=" N THR I 166 " --> pdb=" O ASN I 214 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS I 215 " --> pdb=" O THR I 220 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 27 through 32 removed outlier: 3.510A pdb=" N SER C 32 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER C 61 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ASN C 62 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR C 269 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER C 95 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 49 through 56 removed outlier: 3.930A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.565A pdb=" N GLY C 104 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ARG C 103 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C 168 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 317 through 320 removed outlier: 4.260A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.600A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.655A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.906A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.720A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.720A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.254A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 1120 through 1122 1278 hydrogen bonds defined for protein. 3423 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: 9.15 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5697 1.30 - 1.43: 9579 1.43 - 1.56: 20334 1.56 - 1.69: 0 1.69 - 1.82: 204 Bond restraints: 35814 Sorted by residual: bond pdb=" CA ARG B 328 " pdb=" C ARG B 328 " ideal model delta sigma weight residual 1.525 1.438 0.087 1.28e-02 6.10e+03 4.61e+01 bond pdb=" C PHE B 329 " pdb=" O PHE B 329 " ideal model delta sigma weight residual 1.241 1.168 0.073 1.23e-02 6.61e+03 3.56e+01 bond pdb=" N PHE B 329 " pdb=" CA PHE B 329 " ideal model delta sigma weight residual 1.462 1.407 0.056 1.07e-02 8.73e+03 2.73e+01 bond pdb=" C CYS C 336 " pdb=" N PRO C 337 " ideal model delta sigma weight residual 1.331 1.392 -0.061 1.21e-02 6.83e+03 2.51e+01 bond pdb=" CA CYS C 525 " pdb=" C CYS C 525 " ideal model delta sigma weight residual 1.530 1.478 0.052 1.23e-02 6.61e+03 1.82e+01 ... (remaining 35809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 48542 2.94 - 5.87: 205 5.87 - 8.81: 27 8.81 - 11.74: 6 11.74 - 14.68: 3 Bond angle restraints: 48783 Sorted by residual: angle pdb=" N THR B 333 " pdb=" CA THR B 333 " pdb=" C THR B 333 " ideal model delta sigma weight residual 108.74 123.42 -14.68 1.38e+00 5.25e-01 1.13e+02 angle pdb=" N CYS C 336 " pdb=" CA CYS C 336 " pdb=" C CYS C 336 " ideal model delta sigma weight residual 108.55 122.00 -13.45 1.56e+00 4.11e-01 7.43e+01 angle pdb=" C GLY G 133 " pdb=" N PRO G 134 " pdb=" CA PRO G 134 " ideal model delta sigma weight residual 119.85 112.41 7.44 1.01e+00 9.80e-01 5.43e+01 angle pdb=" N LEU B 335 " pdb=" CA LEU B 335 " pdb=" C LEU B 335 " ideal model delta sigma weight residual 110.33 119.38 -9.05 1.29e+00 6.01e-01 4.93e+01 angle pdb=" N ALA J 132 " pdb=" CA ALA J 132 " pdb=" C ALA J 132 " ideal model delta sigma weight residual 108.34 117.13 -8.79 1.31e+00 5.83e-01 4.51e+01 ... (remaining 48778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.19: 20401 14.19 - 28.37: 736 28.37 - 42.56: 149 42.56 - 56.74: 47 56.74 - 70.93: 12 Dihedral angle restraints: 21345 sinusoidal: 8223 harmonic: 13122 Sorted by residual: dihedral pdb=" N ASN C 331 " pdb=" C ASN C 331 " pdb=" CA ASN C 331 " pdb=" CB ASN C 331 " ideal model delta harmonic sigma weight residual 122.80 136.94 -14.14 0 2.50e+00 1.60e-01 3.20e+01 dihedral pdb=" C ASN C 331 " pdb=" N ASN C 331 " pdb=" CA ASN C 331 " pdb=" CB ASN C 331 " ideal model delta harmonic sigma weight residual -122.60 -136.13 13.53 0 2.50e+00 1.60e-01 2.93e+01 dihedral pdb=" CA VAL G 126 " pdb=" C VAL G 126 " pdb=" N SER G 127 " pdb=" CA SER G 127 " ideal model delta harmonic sigma weight residual -180.00 -155.94 -24.06 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 21342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 5453 0.126 - 0.253: 22 0.253 - 0.379: 8 0.379 - 0.506: 0 0.506 - 0.632: 1 Chirality restraints: 5484 Sorted by residual: chirality pdb=" CA ASN C 331 " pdb=" N ASN C 331 " pdb=" C ASN C 331 " pdb=" CB ASN C 331 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA LEU B 335 " pdb=" N LEU B 335 " pdb=" C LEU B 335 " pdb=" CB LEU B 335 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA SER G 127 " pdb=" N SER G 127 " pdb=" C SER G 127 " pdb=" CB SER G 127 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 5481 not shown) Planarity restraints: 6288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 328 " -0.026 2.00e-02 2.50e+03 5.33e-02 2.84e+01 pdb=" C ARG C 328 " 0.092 2.00e-02 2.50e+03 pdb=" O ARG C 328 " -0.036 2.00e-02 2.50e+03 pdb=" N PHE C 329 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN J 129 " -0.061 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO J 130 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO J 130 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO J 130 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 327 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.07e+00 pdb=" C VAL B 327 " -0.046 2.00e-02 2.50e+03 pdb=" O VAL B 327 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG B 328 " 0.016 2.00e-02 2.50e+03 ... (remaining 6285 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6162 2.77 - 3.30: 31785 3.30 - 3.84: 56503 3.84 - 4.37: 65424 4.37 - 4.90: 115722 Nonbonded interactions: 275596 Sorted by model distance: nonbonded pdb=" O ALA J 171 " pdb=" OG SER J 174 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.245 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.246 3.040 nonbonded pdb=" O ALA K 171 " pdb=" OG SER K 174 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.248 3.040 ... (remaining 275591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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 individual isotropic 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: 7.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 34.690 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 35868 Z= 0.158 Angle : 0.573 14.678 48891 Z= 0.341 Chirality : 0.044 0.632 5484 Planarity : 0.004 0.093 6288 Dihedral : 7.849 70.927 12777 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.30 % Favored : 95.55 % Rotamer: Outliers : 2.77 % Allowed : 5.03 % Favored : 92.21 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.62 (0.11), residues: 4470 helix: -1.24 (0.16), residues: 639 sheet: -0.75 (0.14), residues: 1110 loop : -2.42 (0.10), residues: 2721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 273 TYR 0.005 0.000 TYR B 453 PHE 0.014 0.001 PHE C 329 TRP 0.006 0.000 TRP H 91 HIS 0.001 0.000 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00229 (35814) covalent geometry : angle 0.57214 (48783) SS BOND : bond 0.00289 ( 54) SS BOND : angle 0.79387 ( 108) hydrogen bonds : bond 0.26115 ( 1233) hydrogen bonds : angle 8.92911 ( 3423) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 521 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.8283 (tpt) cc_final: 0.8058 (tpp) REVERT: B 780 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7779 (mt-10) REVERT: B 988 GLU cc_start: 0.8648 (tp30) cc_final: 0.8442 (tp30) REVERT: B 1002 GLN cc_start: 0.7880 (tt0) cc_final: 0.7521 (tt0) REVERT: A 89 ASP cc_start: 0.8150 (m-30) cc_final: 0.7949 (p0) REVERT: A 340 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7784 (mp0) REVERT: A 364 ASP cc_start: 0.7992 (t0) cc_final: 0.7704 (t0) REVERT: A 421 TYR cc_start: 0.4939 (m-10) cc_final: 0.4711 (m-10) REVERT: A 429 PHE cc_start: 0.7519 (t80) cc_final: 0.7266 (t80) REVERT: A 456 LEU cc_start: 0.5922 (mt) cc_final: 0.5653 (mm) REVERT: A 592 PHE cc_start: 0.7244 (t80) cc_final: 0.6575 (t80) REVERT: J 43 GLN cc_start: 0.8023 (tt0) cc_final: 0.7095 (tt0) REVERT: J 55 TYR cc_start: 0.8276 (p90) cc_final: 0.7528 (p90) REVERT: J 66 LYS cc_start: 0.8243 (mttp) cc_final: 0.7817 (mmtt) REVERT: J 80 LYS cc_start: 0.3317 (tttt) cc_final: 0.2054 (mttm) REVERT: J 118 PHE cc_start: 0.2989 (m-80) cc_final: 0.2309 (m-80) REVERT: J 159 ASP cc_start: 0.9358 (m-30) cc_final: 0.9127 (t0) REVERT: J 201 LEU cc_start: 0.1082 (OUTLIER) cc_final: 0.0793 (mt) REVERT: G 53 MET cc_start: 0.6279 (mtm) cc_final: 0.5822 (mpp) REVERT: G 117 TYR cc_start: 0.8602 (m-80) cc_final: 0.8269 (m-10) REVERT: K 103 TYR cc_start: 0.6933 (m-80) cc_final: 0.6484 (m-80) REVERT: L 215 GLN cc_start: 0.8465 (tp40) cc_final: 0.8119 (tp40) REVERT: I 43 ARG cc_start: 0.7516 (ttm170) cc_final: 0.7289 (ttm170) REVERT: I 89 LEU cc_start: 0.7129 (tp) cc_final: 0.5910 (tt) REVERT: I 109 ASP cc_start: 0.7179 (m-30) cc_final: 0.6639 (t0) REVERT: I 115 LEU cc_start: 0.8046 (mt) cc_final: 0.7546 (mp) REVERT: I 163 GLU cc_start: 0.8382 (tp30) cc_final: 0.8144 (tp30) REVERT: C 80 PHE cc_start: 0.5865 (m-10) cc_final: 0.5361 (m-10) REVERT: C 165 ASN cc_start: 0.8212 (m-40) cc_final: 0.7842 (p0) REVERT: C 320 VAL cc_start: 0.7417 (OUTLIER) cc_final: 0.7175 (p) REVERT: C 462 LYS cc_start: 0.9436 (mttm) cc_final: 0.9125 (mptt) REVERT: C 498 ARG cc_start: 0.9090 (mtt180) cc_final: 0.8823 (mmt90) REVERT: C 904 TYR cc_start: 0.7316 (m-80) cc_final: 0.6992 (m-10) REVERT: C 1005 GLN cc_start: 0.7984 (mt0) cc_final: 0.7610 (mt0) outliers start: 108 outliers final: 18 residues processed: 610 average time/residue: 0.2581 time to fit residues: 244.6577 Evaluate side-chains 307 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 287 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 811 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 31 ASN B 88 ASN B 100 ASN B 185 ASN B 239 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 414 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 677 GLN B 690 GLN B 762 GLN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 957 GLN B1011 GLN A 27 GLN A 88 ASN A 100 ASN A 185 ASN A 239 GLN A 321 GLN A 339 HIS A 414 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 607 GLN A 677 GLN A 690 GLN A 836 GLN A 955 ASN A 957 GLN A 965 GLN A1002 GLN A1011 GLN J 17 GLN J 95 GLN ** J 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN K 95 GLN H 75 GLN L 95 GLN L 205 GLN L 209 HIS L 218 HIS I 90 HIS ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN C 31 ASN C 88 ASN C 185 ASN C 239 GLN ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 354 ASN C 414 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 536 ASN C 544 ASN C 607 GLN C 677 GLN ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 957 GLN C1011 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.101005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.068121 restraints weight = 130230.372| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 4.19 r_work: 0.3201 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35868 Z= 0.167 Angle : 0.627 16.005 48891 Z= 0.321 Chirality : 0.045 0.188 5484 Planarity : 0.005 0.106 6288 Dihedral : 4.392 54.213 4894 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 1.82 % Allowed : 9.51 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.47 (0.12), residues: 4470 helix: 1.12 (0.19), residues: 675 sheet: -0.19 (0.14), residues: 1135 loop : -2.01 (0.11), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 457 TYR 0.018 0.001 TYR H 102 PHE 0.022 0.001 PHE A 400 TRP 0.018 0.001 TRP G 41 HIS 0.014 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00372 (35814) covalent geometry : angle 0.62684 (48783) SS BOND : bond 0.00288 ( 54) SS BOND : angle 0.78201 ( 108) hydrogen bonds : bond 0.05002 ( 1233) hydrogen bonds : angle 6.32011 ( 3423) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 282 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 515 PHE cc_start: 0.7638 (m-80) cc_final: 0.7293 (m-80) REVERT: B 592 PHE cc_start: 0.7657 (t80) cc_final: 0.7281 (t80) REVERT: B 844 ILE cc_start: 0.6019 (OUTLIER) cc_final: 0.5814 (tp) REVERT: A 364 ASP cc_start: 0.8308 (t0) cc_final: 0.8000 (t0) REVERT: A 429 PHE cc_start: 0.7825 (t80) cc_final: 0.7611 (t80) REVERT: J 66 LYS cc_start: 0.8471 (mttp) cc_final: 0.8069 (mmtt) REVERT: J 80 LYS cc_start: 0.4166 (tttt) cc_final: 0.2508 (mttt) REVERT: J 159 ASP cc_start: 0.9345 (m-30) cc_final: 0.9046 (t0) REVERT: J 177 LYS cc_start: 0.6394 (mmtm) cc_final: 0.5789 (mmmt) REVERT: J 201 LEU cc_start: 0.0610 (OUTLIER) cc_final: 0.0222 (mt) REVERT: G 53 MET cc_start: 0.5872 (mtm) cc_final: 0.4934 (mpp) REVERT: K 103 TYR cc_start: 0.7029 (m-80) cc_final: 0.6658 (m-80) REVERT: H 45 MET cc_start: 0.7745 (mmm) cc_final: 0.7251 (mmm) REVERT: H 91 TRP cc_start: 0.6194 (OUTLIER) cc_final: 0.5678 (m-10) REVERT: L 53 MET cc_start: 0.8035 (mmm) cc_final: 0.7726 (mmm) REVERT: I 43 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7518 (ttt180) REVERT: I 109 ASP cc_start: 0.7712 (m-30) cc_final: 0.6976 (t0) REVERT: I 112 TRP cc_start: 0.7443 (p-90) cc_final: 0.7055 (p-90) REVERT: I 163 GLU cc_start: 0.8451 (tp30) cc_final: 0.8044 (tp30) REVERT: C 153 MET cc_start: 0.7411 (pmm) cc_final: 0.7154 (pmm) REVERT: C 165 ASN cc_start: 0.8510 (m-40) cc_final: 0.7923 (p0) REVERT: C 335 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8409 (tm) REVERT: C 462 LYS cc_start: 0.9512 (mttm) cc_final: 0.9138 (mptt) REVERT: C 498 ARG cc_start: 0.9181 (mtt180) cc_final: 0.8766 (mmm-85) REVERT: C 587 ILE cc_start: 0.8873 (mm) cc_final: 0.8673 (tp) REVERT: C 636 TYR cc_start: 0.7310 (m-80) cc_final: 0.7076 (m-10) REVERT: C 1002 GLN cc_start: 0.9133 (tt0) cc_final: 0.8910 (tt0) outliers start: 71 outliers final: 31 residues processed: 336 average time/residue: 0.2349 time to fit residues: 126.7422 Evaluate side-chains 264 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain K residue 36 TYR Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain H residue 91 TRP Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain L residue 170 LYS Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 133 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 339 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 373 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 221 optimal weight: 8.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN A 31 ASN A 67 HIS A 188 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN A1005 GLN ** J 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 HIS ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 616 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.096230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.062003 restraints weight = 129403.379| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 4.20 r_work: 0.3059 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 35868 Z= 0.233 Angle : 0.654 13.135 48891 Z= 0.334 Chirality : 0.046 0.197 5484 Planarity : 0.005 0.094 6288 Dihedral : 4.915 58.702 4879 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.35 % Favored : 93.56 % Rotamer: Outliers : 2.28 % Allowed : 9.41 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.06 (0.12), residues: 4470 helix: 1.91 (0.21), residues: 642 sheet: -0.08 (0.15), residues: 1154 loop : -1.74 (0.11), residues: 2674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 454 TYR 0.030 0.002 TYR B 160 PHE 0.029 0.002 PHE A 80 TRP 0.031 0.002 TRP I 41 HIS 0.007 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00518 (35814) covalent geometry : angle 0.65305 (48783) SS BOND : bond 0.00333 ( 54) SS BOND : angle 0.89127 ( 108) hydrogen bonds : bond 0.04602 ( 1233) hydrogen bonds : angle 5.73976 ( 3423) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 244 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 ASN cc_start: 0.8693 (t0) cc_final: 0.8221 (p0) REVERT: B 740 MET cc_start: 0.9200 (tpp) cc_final: 0.8932 (tpp) REVERT: B 780 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8730 (mt-10) REVERT: B 988 GLU cc_start: 0.8971 (mp0) cc_final: 0.8714 (mp0) REVERT: B 1092 GLU cc_start: 0.8897 (pm20) cc_final: 0.8674 (pp20) REVERT: A 330 PRO cc_start: 0.6376 (Cg_exo) cc_final: 0.6152 (Cg_endo) REVERT: A 453 TYR cc_start: 0.4178 (p90) cc_final: 0.3897 (p90) REVERT: J 43 GLN cc_start: 0.7471 (tt0) cc_final: 0.7244 (tt0) REVERT: J 66 LYS cc_start: 0.8543 (mttp) cc_final: 0.8159 (mmtt) REVERT: J 80 LYS cc_start: 0.4482 (tttt) cc_final: 0.2732 (mttt) REVERT: J 159 ASP cc_start: 0.9305 (m-30) cc_final: 0.8949 (t0) REVERT: J 177 LYS cc_start: 0.6411 (mmtm) cc_final: 0.6062 (mmmt) REVERT: J 201 LEU cc_start: 0.0257 (OUTLIER) cc_final: 0.0028 (mt) REVERT: G 53 MET cc_start: 0.5262 (mtm) cc_final: 0.4791 (mpp) REVERT: K 103 TYR cc_start: 0.6981 (m-80) cc_final: 0.6516 (m-10) REVERT: L 109 LEU cc_start: 0.9245 (tt) cc_final: 0.8934 (mm) REVERT: L 161 TYR cc_start: 0.9557 (t80) cc_final: 0.9146 (t80) REVERT: I 45 MET cc_start: 0.8559 (mmp) cc_final: 0.8254 (mmm) REVERT: I 53 MET cc_start: 0.6164 (ptp) cc_final: 0.5938 (ptp) REVERT: I 109 ASP cc_start: 0.7743 (m-30) cc_final: 0.7020 (t0) REVERT: I 163 GLU cc_start: 0.8429 (tp30) cc_final: 0.8054 (tp30) REVERT: C 153 MET cc_start: 0.8318 (pmm) cc_final: 0.8025 (pmm) REVERT: C 198 ASP cc_start: 0.8646 (t0) cc_final: 0.8368 (t0) REVERT: C 318 PHE cc_start: 0.7182 (p90) cc_final: 0.6965 (p90) REVERT: C 328 ARG cc_start: 0.8301 (mtm180) cc_final: 0.7777 (mtm180) REVERT: C 462 LYS cc_start: 0.9524 (mttm) cc_final: 0.9112 (mptt) REVERT: C 493 GLN cc_start: 0.8562 (tp-100) cc_final: 0.8187 (tp-100) REVERT: C 498 ARG cc_start: 0.9221 (mtt180) cc_final: 0.8765 (mmm-85) REVERT: C 516 GLU cc_start: 0.8782 (tp30) cc_final: 0.8385 (tp30) outliers start: 89 outliers final: 43 residues processed: 315 average time/residue: 0.2309 time to fit residues: 117.3464 Evaluate side-chains 259 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain K residue 36 TYR Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 170 LYS Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 75 GLN Chi-restraints excluded: chain I residue 92 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 7 optimal weight: 4.9990 chunk 393 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 195 optimal weight: 0.5980 chunk 371 optimal weight: 0.8980 chunk 357 optimal weight: 0.7980 chunk 331 optimal weight: 20.0000 chunk 162 optimal weight: 0.9980 chunk 283 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN A 100 ASN A 343 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 205 GLN L 215 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.096800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.062970 restraints weight = 127988.425| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 4.18 r_work: 0.3079 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35868 Z= 0.130 Angle : 0.572 15.307 48891 Z= 0.290 Chirality : 0.044 0.238 5484 Planarity : 0.004 0.080 6288 Dihedral : 4.724 59.309 4878 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.00 % Favored : 93.96 % Rotamer: Outliers : 1.62 % Allowed : 10.67 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.12), residues: 4470 helix: 2.20 (0.21), residues: 639 sheet: 0.09 (0.15), residues: 1116 loop : -1.59 (0.11), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 983 TYR 0.038 0.001 TYR G 117 PHE 0.033 0.001 PHE C 338 TRP 0.027 0.001 TRP G 41 HIS 0.003 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00290 (35814) covalent geometry : angle 0.56864 (48783) SS BOND : bond 0.00231 ( 54) SS BOND : angle 1.37732 ( 108) hydrogen bonds : bond 0.03915 ( 1233) hydrogen bonds : angle 5.47903 ( 3423) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 222 time to evaluate : 1.327 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: B 138 ASN cc_start: 0.8676 (t0) cc_final: 0.8226 (p0) REVERT: B 780 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8721 (mt-10) REVERT: B 988 GLU cc_start: 0.8968 (mp0) cc_final: 0.8683 (mp0) REVERT: B 990 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8308 (pp20) REVERT: B 1092 GLU cc_start: 0.8830 (pm20) cc_final: 0.8621 (pp20) REVERT: A 423 TYR cc_start: 0.7162 (t80) cc_final: 0.6864 (t80) REVERT: A 425 LEU cc_start: 0.9076 (tp) cc_final: 0.8792 (tp) REVERT: A 453 TYR cc_start: 0.4005 (p90) cc_final: 0.3524 (p90) REVERT: A 988 GLU cc_start: 0.8782 (mp0) cc_final: 0.8556 (mp0) REVERT: J 66 LYS cc_start: 0.8553 (mttp) cc_final: 0.8179 (mmtt) REVERT: J 80 LYS cc_start: 0.4373 (tttt) cc_final: 0.2664 (mttt) REVERT: J 159 ASP cc_start: 0.9320 (m-30) cc_final: 0.8956 (t0) REVERT: J 177 LYS cc_start: 0.6414 (mmtm) cc_final: 0.6062 (mmmt) REVERT: J 201 LEU cc_start: 0.0523 (OUTLIER) cc_final: 0.0162 (mt) REVERT: G 2 MET cc_start: 0.6397 (tmm) cc_final: 0.5324 (tmm) REVERT: L 53 MET cc_start: 0.7955 (mmm) cc_final: 0.7668 (mmm) REVERT: L 109 LEU cc_start: 0.9242 (tt) cc_final: 0.8926 (mm) REVERT: I 109 ASP cc_start: 0.7800 (m-30) cc_final: 0.7209 (t0) REVERT: I 112 TRP cc_start: 0.8097 (p-90) cc_final: 0.7885 (p-90) REVERT: I 163 GLU cc_start: 0.8453 (tp30) cc_final: 0.8062 (tp30) REVERT: C 153 MET cc_start: 0.8227 (pmm) cc_final: 0.7934 (pmm) REVERT: C 198 ASP cc_start: 0.8714 (t0) cc_final: 0.8420 (t0) REVERT: C 328 ARG cc_start: 0.8248 (mtm180) cc_final: 0.7772 (mtm180) REVERT: C 462 LYS cc_start: 0.9537 (mttm) cc_final: 0.9143 (mptt) REVERT: C 493 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8332 (tp-100) REVERT: C 498 ARG cc_start: 0.9204 (mtt180) cc_final: 0.8698 (mmm-85) REVERT: C 740 MET cc_start: 0.9081 (tpp) cc_final: 0.8839 (tpp) outliers start: 63 outliers final: 37 residues processed: 273 average time/residue: 0.2173 time to fit residues: 95.7912 Evaluate side-chains 245 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain J residue 129 GLN Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain G residue 90 HIS Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain K residue 36 TYR Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain L residue 170 LYS Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 70 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 chunk 216 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 433 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 chunk 443 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 213 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** J 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 218 HIS L 205 GLN L 215 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 188 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.096338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.062560 restraints weight = 130670.414| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 4.21 r_work: 0.3065 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35868 Z= 0.134 Angle : 0.555 10.223 48891 Z= 0.282 Chirality : 0.044 0.171 5484 Planarity : 0.004 0.079 6288 Dihedral : 4.701 59.940 4873 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.60 % Favored : 93.36 % Rotamer: Outliers : 1.79 % Allowed : 11.31 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.12), residues: 4470 helix: 2.32 (0.21), residues: 639 sheet: 0.12 (0.15), residues: 1131 loop : -1.48 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 43 TYR 0.030 0.001 TYR K 103 PHE 0.030 0.001 PHE C 338 TRP 0.016 0.001 TRP G 41 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00301 (35814) covalent geometry : angle 0.55336 (48783) SS BOND : bond 0.00258 ( 54) SS BOND : angle 1.06874 ( 108) hydrogen bonds : bond 0.03764 ( 1233) hydrogen bonds : angle 5.30423 ( 3423) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 217 time to evaluate : 1.304 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: B 138 ASN cc_start: 0.8717 (t0) cc_final: 0.8234 (p0) REVERT: B 780 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8718 (mt-10) REVERT: B 988 GLU cc_start: 0.9009 (mp0) cc_final: 0.8734 (mp0) REVERT: B 990 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8338 (pp20) REVERT: A 425 LEU cc_start: 0.9164 (tp) cc_final: 0.8878 (tp) REVERT: A 453 TYR cc_start: 0.4307 (p90) cc_final: 0.3870 (p90) REVERT: A 461 LEU cc_start: 0.6729 (tp) cc_final: 0.6356 (tp) REVERT: A 592 PHE cc_start: 0.8029 (t80) cc_final: 0.7617 (t80) REVERT: A 837 TYR cc_start: 0.8267 (t80) cc_final: 0.7887 (t80) REVERT: A 988 GLU cc_start: 0.8787 (mp0) cc_final: 0.8546 (mp0) REVERT: J 66 LYS cc_start: 0.8540 (mttp) cc_final: 0.8154 (mmtt) REVERT: J 80 LYS cc_start: 0.4551 (tttt) cc_final: 0.2668 (mtmm) REVERT: J 159 ASP cc_start: 0.9306 (m-30) cc_final: 0.8921 (t0) REVERT: J 177 LYS cc_start: 0.6432 (mmtm) cc_final: 0.6091 (mmmt) REVERT: J 201 LEU cc_start: -0.0065 (OUTLIER) cc_final: -0.0354 (mt) REVERT: G 53 MET cc_start: 0.5852 (ptp) cc_final: 0.5434 (mpp) REVERT: H 43 ARG cc_start: 0.7761 (ttm110) cc_final: 0.7281 (ttm-80) REVERT: H 81 ASP cc_start: 0.6302 (OUTLIER) cc_final: 0.5370 (p0) REVERT: H 88 TYR cc_start: 0.7009 (m-80) cc_final: 0.6789 (m-10) REVERT: L 53 MET cc_start: 0.7956 (mmm) cc_final: 0.7478 (mmt) REVERT: L 109 LEU cc_start: 0.9245 (tt) cc_final: 0.8904 (mm) REVERT: I 163 GLU cc_start: 0.8463 (tp30) cc_final: 0.8064 (tp30) REVERT: C 153 MET cc_start: 0.8360 (pmm) cc_final: 0.8078 (pmm) REVERT: C 198 ASP cc_start: 0.8698 (t0) cc_final: 0.8378 (t0) REVERT: C 328 ARG cc_start: 0.8323 (mtm180) cc_final: 0.7816 (mtm180) REVERT: C 462 LYS cc_start: 0.9556 (mttm) cc_final: 0.9169 (mptt) REVERT: C 498 ARG cc_start: 0.9196 (mtt180) cc_final: 0.8689 (mmm-85) outliers start: 70 outliers final: 41 residues processed: 276 average time/residue: 0.2219 time to fit residues: 99.1799 Evaluate side-chains 248 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain J residue 129 GLN Chi-restraints excluded: chain J residue 131 LYS Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain K residue 36 TYR Chi-restraints excluded: chain K residue 76 PHE Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain L residue 170 LYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 129 optimal weight: 0.9990 chunk 445 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 333 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 356 optimal weight: 6.9990 chunk 427 optimal weight: 3.9990 chunk 400 optimal weight: 0.8980 chunk 206 optimal weight: 0.6980 chunk 382 optimal weight: 0.0050 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** J 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 215 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.096122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.062559 restraints weight = 128080.019| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 4.14 r_work: 0.3072 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35868 Z= 0.118 Angle : 0.541 9.938 48891 Z= 0.274 Chirality : 0.044 0.225 5484 Planarity : 0.004 0.068 6288 Dihedral : 4.682 59.294 4873 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.51 % Favored : 93.45 % Rotamer: Outliers : 1.82 % Allowed : 11.33 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.13), residues: 4470 helix: 2.45 (0.21), residues: 639 sheet: 0.16 (0.15), residues: 1140 loop : -1.39 (0.12), residues: 2691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 328 TYR 0.034 0.001 TYR K 103 PHE 0.024 0.001 PHE C 338 TRP 0.015 0.001 TRP I 112 HIS 0.003 0.000 HIS L 209 Details of bonding type rmsd covalent geometry : bond 0.00263 (35814) covalent geometry : angle 0.54037 (48783) SS BOND : bond 0.00299 ( 54) SS BOND : angle 0.80841 ( 108) hydrogen bonds : bond 0.03562 ( 1233) hydrogen bonds : angle 5.16454 ( 3423) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 216 time to evaluate : 1.302 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: B 740 MET cc_start: 0.8873 (ttm) cc_final: 0.8222 (ttm) REVERT: B 780 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8618 (mt-10) REVERT: B 988 GLU cc_start: 0.8923 (mp0) cc_final: 0.8657 (mp0) REVERT: B 990 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8311 (pp20) REVERT: A 453 TYR cc_start: 0.4427 (p90) cc_final: 0.4014 (p90) REVERT: A 461 LEU cc_start: 0.6637 (tp) cc_final: 0.6287 (tp) REVERT: A 837 TYR cc_start: 0.8070 (t80) cc_final: 0.7762 (t80) REVERT: A 988 GLU cc_start: 0.8779 (mp0) cc_final: 0.8552 (mp0) REVERT: J 66 LYS cc_start: 0.8524 (mttp) cc_final: 0.8119 (mmtt) REVERT: J 80 LYS cc_start: 0.4600 (tttt) cc_final: 0.2662 (mtmm) REVERT: J 159 ASP cc_start: 0.9302 (m-30) cc_final: 0.8925 (t0) REVERT: J 177 LYS cc_start: 0.6398 (mmtm) cc_final: 0.6049 (mmmt) REVERT: J 201 LEU cc_start: 0.0114 (OUTLIER) cc_final: -0.0209 (mt) REVERT: G 2 MET cc_start: 0.5714 (tmm) cc_final: 0.4967 (tmm) REVERT: G 53 MET cc_start: 0.5760 (ptp) cc_final: 0.5247 (mpp) REVERT: K 53 MET cc_start: 0.3043 (mmm) cc_final: 0.2839 (mmm) REVERT: H 81 ASP cc_start: 0.6271 (OUTLIER) cc_final: 0.5337 (p0) REVERT: L 53 MET cc_start: 0.7945 (mmm) cc_final: 0.7629 (mmm) REVERT: L 109 LEU cc_start: 0.9234 (tt) cc_final: 0.8927 (mm) REVERT: I 163 GLU cc_start: 0.8444 (tp30) cc_final: 0.8042 (tp30) REVERT: C 153 MET cc_start: 0.8349 (pmm) cc_final: 0.8078 (pmm) REVERT: C 198 ASP cc_start: 0.8635 (t0) cc_final: 0.8411 (t0) REVERT: C 328 ARG cc_start: 0.8317 (mtm180) cc_final: 0.7823 (mtm180) REVERT: C 462 LYS cc_start: 0.9573 (mttm) cc_final: 0.9172 (mptt) REVERT: C 498 ARG cc_start: 0.9189 (mtt180) cc_final: 0.8678 (mmm-85) outliers start: 71 outliers final: 54 residues processed: 275 average time/residue: 0.2240 time to fit residues: 100.3652 Evaluate side-chains 263 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain J residue 129 GLN Chi-restraints excluded: chain J residue 131 LYS Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain K residue 36 TYR Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 170 LYS Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 83 optimal weight: 2.9990 chunk 370 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 419 optimal weight: 0.4980 chunk 330 optimal weight: 20.0000 chunk 425 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 362 optimal weight: 3.9990 chunk 252 optimal weight: 0.0770 chunk 155 optimal weight: 3.9990 chunk 239 optimal weight: 9.9990 overall best weight: 1.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 965 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** J 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN H 90 HIS L 45 HIS L 205 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 343 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** 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 = 0.4001 r_free = 0.4001 target = 0.093780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.060046 restraints weight = 128245.147| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 4.09 r_work: 0.3012 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35868 Z= 0.186 Angle : 0.597 10.663 48891 Z= 0.305 Chirality : 0.045 0.227 5484 Planarity : 0.004 0.080 6288 Dihedral : 4.964 59.870 4873 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.87 % Favored : 93.09 % Rotamer: Outliers : 1.95 % Allowed : 11.46 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.13), residues: 4470 helix: 2.12 (0.21), residues: 663 sheet: 0.09 (0.15), residues: 1163 loop : -1.39 (0.12), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 328 TYR 0.039 0.002 TYR C 904 PHE 0.024 0.001 PHE C 338 TRP 0.016 0.001 TRP G 118 HIS 0.005 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00420 (35814) covalent geometry : angle 0.59581 (48783) SS BOND : bond 0.00305 ( 54) SS BOND : angle 0.93312 ( 108) hydrogen bonds : bond 0.04000 ( 1233) hydrogen bonds : angle 5.27450 ( 3423) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 221 time to evaluate : 1.204 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: B 329 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7381 (t80) REVERT: B 780 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8727 (mt-10) REVERT: B 988 GLU cc_start: 0.8948 (mp0) cc_final: 0.8599 (mp0) REVERT: A 321 GLN cc_start: 0.8196 (tp40) cc_final: 0.7895 (tp40) REVERT: A 366 SER cc_start: 0.9232 (m) cc_final: 0.8996 (p) REVERT: A 453 TYR cc_start: 0.4868 (p90) cc_final: 0.4230 (p90) REVERT: A 461 LEU cc_start: 0.7292 (tp) cc_final: 0.7044 (tp) REVERT: A 837 TYR cc_start: 0.8158 (t80) cc_final: 0.7807 (t80) REVERT: A 988 GLU cc_start: 0.8897 (mp0) cc_final: 0.8632 (mp0) REVERT: J 48 LYS cc_start: 0.7552 (tptp) cc_final: 0.6560 (ptpp) REVERT: J 66 LYS cc_start: 0.8665 (mttp) cc_final: 0.8287 (mmtt) REVERT: J 80 LYS cc_start: 0.5093 (tttt) cc_final: 0.3047 (mtmm) REVERT: J 159 ASP cc_start: 0.9338 (m-30) cc_final: 0.8957 (t0) REVERT: J 177 LYS cc_start: 0.6324 (mmtm) cc_final: 0.5981 (mmmt) REVERT: G 53 MET cc_start: 0.5790 (ptp) cc_final: 0.5166 (mpp) REVERT: H 43 ARG cc_start: 0.7861 (ttm110) cc_final: 0.7155 (ttm-80) REVERT: H 81 ASP cc_start: 0.5838 (OUTLIER) cc_final: 0.5554 (p0) REVERT: L 53 MET cc_start: 0.8035 (mmm) cc_final: 0.7710 (mmm) REVERT: L 109 LEU cc_start: 0.9279 (tt) cc_final: 0.8905 (mm) REVERT: I 163 GLU cc_start: 0.8477 (tp30) cc_final: 0.8077 (tp30) REVERT: C 153 MET cc_start: 0.8622 (pmm) cc_final: 0.8360 (pmm) REVERT: C 198 ASP cc_start: 0.8591 (t0) cc_final: 0.8360 (t0) REVERT: C 328 ARG cc_start: 0.8462 (mtm180) cc_final: 0.7944 (mtm180) REVERT: C 462 LYS cc_start: 0.9585 (mttm) cc_final: 0.9191 (mptt) REVERT: C 498 ARG cc_start: 0.9166 (mtt180) cc_final: 0.8556 (mmt90) outliers start: 76 outliers final: 58 residues processed: 282 average time/residue: 0.2125 time to fit residues: 96.5783 Evaluate side-chains 265 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 205 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain J residue 129 GLN Chi-restraints excluded: chain J residue 131 LYS Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain K residue 76 PHE Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain L residue 170 LYS Chi-restraints excluded: chain I residue 75 GLN Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 92 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 278 optimal weight: 0.0050 chunk 355 optimal weight: 0.0770 chunk 295 optimal weight: 8.9990 chunk 364 optimal weight: 0.8980 chunk 385 optimal weight: 6.9990 chunk 280 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.5752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 965 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** K 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.094693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.060266 restraints weight = 127235.834| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 4.22 r_work: 0.3011 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35868 Z= 0.115 Angle : 0.561 10.157 48891 Z= 0.286 Chirality : 0.044 0.343 5484 Planarity : 0.004 0.073 6288 Dihedral : 4.818 59.988 4873 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.47 % Favored : 93.49 % Rotamer: Outliers : 1.64 % Allowed : 12.00 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 4470 helix: 2.11 (0.21), residues: 681 sheet: 0.16 (0.15), residues: 1162 loop : -1.35 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 106 TYR 0.019 0.001 TYR A 904 PHE 0.017 0.001 PHE A 592 TRP 0.040 0.001 TRP I 112 HIS 0.003 0.000 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00258 (35814) covalent geometry : angle 0.56029 (48783) SS BOND : bond 0.00255 ( 54) SS BOND : angle 0.77173 ( 108) hydrogen bonds : bond 0.03538 ( 1233) hydrogen bonds : angle 5.09200 ( 3423) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 218 time to evaluate : 1.215 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: B 328 ARG cc_start: 0.7044 (tpt170) cc_final: 0.6720 (tpt170) REVERT: B 329 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.7028 (t80) REVERT: B 780 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8786 (mt-10) REVERT: B 988 GLU cc_start: 0.9035 (mp0) cc_final: 0.8679 (mp0) REVERT: A 321 GLN cc_start: 0.8066 (tp40) cc_final: 0.7738 (tp40) REVERT: A 328 ARG cc_start: 0.6496 (tpt170) cc_final: 0.6293 (tpt170) REVERT: A 366 SER cc_start: 0.9272 (m) cc_final: 0.9049 (p) REVERT: A 461 LEU cc_start: 0.7483 (tp) cc_final: 0.7243 (tp) REVERT: A 837 TYR cc_start: 0.8056 (t80) cc_final: 0.7718 (t80) REVERT: A 988 GLU cc_start: 0.8922 (mp0) cc_final: 0.8649 (mp0) REVERT: J 66 LYS cc_start: 0.8694 (mttp) cc_final: 0.8353 (mmtt) REVERT: J 80 LYS cc_start: 0.4793 (tttt) cc_final: 0.2856 (mttt) REVERT: J 159 ASP cc_start: 0.9378 (m-30) cc_final: 0.8988 (t0) REVERT: J 177 LYS cc_start: 0.6342 (mmtm) cc_final: 0.6004 (mmmt) REVERT: G 2 MET cc_start: 0.4523 (tmm) cc_final: 0.3758 (tmm) REVERT: G 53 MET cc_start: 0.5624 (ptp) cc_final: 0.5008 (mpp) REVERT: H 43 ARG cc_start: 0.7883 (ttm110) cc_final: 0.7044 (ttm-80) REVERT: H 81 ASP cc_start: 0.5790 (OUTLIER) cc_final: 0.5542 (p0) REVERT: L 53 MET cc_start: 0.7987 (mmm) cc_final: 0.7668 (mmm) REVERT: L 109 LEU cc_start: 0.9201 (tt) cc_final: 0.8876 (mm) REVERT: I 163 GLU cc_start: 0.8462 (tp30) cc_final: 0.8067 (tp30) REVERT: C 153 MET cc_start: 0.8616 (pmm) cc_final: 0.8333 (pmm) REVERT: C 198 ASP cc_start: 0.8662 (t0) cc_final: 0.8461 (t0) REVERT: C 328 ARG cc_start: 0.8373 (mtm180) cc_final: 0.7833 (mtm180) REVERT: C 365 TYR cc_start: 0.8637 (m-80) cc_final: 0.8403 (m-80) REVERT: C 449 TYR cc_start: 0.8787 (m-80) cc_final: 0.8464 (m-80) REVERT: C 462 LYS cc_start: 0.9587 (mttm) cc_final: 0.9187 (mptt) REVERT: C 498 ARG cc_start: 0.8963 (mtt180) cc_final: 0.8535 (mmt90) outliers start: 64 outliers final: 55 residues processed: 271 average time/residue: 0.2188 time to fit residues: 96.3580 Evaluate side-chains 272 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain J residue 129 GLN Chi-restraints excluded: chain J residue 131 LYS Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain K residue 42 TYR Chi-restraints excluded: chain K residue 76 PHE Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 170 LYS Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 223 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 chunk 365 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 118 optimal weight: 0.0030 chunk 205 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 416 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 chunk 366 optimal weight: 4.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 205 GLN I 3 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.094753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.060630 restraints weight = 127161.312| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 4.20 r_work: 0.3019 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35868 Z= 0.113 Angle : 0.553 10.297 48891 Z= 0.281 Chirality : 0.044 0.284 5484 Planarity : 0.004 0.072 6288 Dihedral : 4.748 59.933 4873 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.76 % Favored : 93.20 % Rotamer: Outliers : 1.69 % Allowed : 12.10 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.13), residues: 4470 helix: 2.38 (0.21), residues: 654 sheet: 0.26 (0.15), residues: 1164 loop : -1.34 (0.12), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 115 TYR 0.024 0.001 TYR C 904 PHE 0.019 0.001 PHE C 338 TRP 0.029 0.001 TRP I 112 HIS 0.002 0.000 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00254 (35814) covalent geometry : angle 0.55228 (48783) SS BOND : bond 0.00230 ( 54) SS BOND : angle 0.72088 ( 108) hydrogen bonds : bond 0.03418 ( 1233) hydrogen bonds : angle 5.00996 ( 3423) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 217 time to evaluate : 1.381 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: B 153 MET cc_start: 0.7967 (pmm) cc_final: 0.7680 (pmm) REVERT: B 313 TYR cc_start: 0.5277 (OUTLIER) cc_final: 0.5027 (t80) REVERT: B 328 ARG cc_start: 0.6994 (tpt170) cc_final: 0.6788 (tpt170) REVERT: B 329 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6814 (t80) REVERT: B 780 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8758 (mt-10) REVERT: B 988 GLU cc_start: 0.9040 (mp0) cc_final: 0.8678 (mp0) REVERT: A 321 GLN cc_start: 0.8112 (tp40) cc_final: 0.7772 (tp40) REVERT: A 366 SER cc_start: 0.9280 (m) cc_final: 0.9065 (p) REVERT: A 461 LEU cc_start: 0.7540 (tp) cc_final: 0.7308 (tp) REVERT: A 516 GLU cc_start: 0.8354 (tp30) cc_final: 0.8104 (tp30) REVERT: A 837 TYR cc_start: 0.8080 (t80) cc_final: 0.7732 (t80) REVERT: A 988 GLU cc_start: 0.8918 (mp0) cc_final: 0.8643 (mp0) REVERT: A 990 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8402 (mm-30) REVERT: J 48 LYS cc_start: 0.7581 (tptp) cc_final: 0.6678 (ptpp) REVERT: J 66 LYS cc_start: 0.8703 (mttp) cc_final: 0.8363 (mmtt) REVERT: J 80 LYS cc_start: 0.4724 (tttt) cc_final: 0.2706 (mttt) REVERT: J 159 ASP cc_start: 0.9383 (m-30) cc_final: 0.8962 (t0) REVERT: J 177 LYS cc_start: 0.6309 (mmtm) cc_final: 0.5962 (mmmt) REVERT: G 2 MET cc_start: 0.4251 (tmm) cc_final: 0.3650 (tmm) REVERT: G 53 MET cc_start: 0.5492 (ptp) cc_final: 0.5047 (mpp) REVERT: G 66 ARG cc_start: 0.8268 (tpp80) cc_final: 0.7890 (tmm160) REVERT: H 43 ARG cc_start: 0.7918 (ttm110) cc_final: 0.7064 (ttm-80) REVERT: H 81 ASP cc_start: 0.5680 (OUTLIER) cc_final: 0.5439 (p0) REVERT: L 53 MET cc_start: 0.7996 (mmm) cc_final: 0.7666 (mmm) REVERT: L 109 LEU cc_start: 0.9185 (tt) cc_final: 0.8902 (mm) REVERT: I 11 GLU cc_start: 0.6299 (mm-30) cc_final: 0.5784 (mm-30) REVERT: I 163 GLU cc_start: 0.8448 (tp30) cc_final: 0.8045 (tp30) REVERT: C 153 MET cc_start: 0.8318 (pmm) cc_final: 0.8009 (pmm) REVERT: C 328 ARG cc_start: 0.8354 (mtm180) cc_final: 0.7808 (mtm180) REVERT: C 462 LYS cc_start: 0.9583 (mttm) cc_final: 0.9184 (mptt) outliers start: 66 outliers final: 45 residues processed: 272 average time/residue: 0.2326 time to fit residues: 102.6047 Evaluate side-chains 256 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 313 TYR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain J residue 129 GLN Chi-restraints excluded: chain J residue 131 LYS Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain K residue 76 PHE Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain L residue 170 LYS Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 171 optimal weight: 2.9990 chunk 362 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 411 optimal weight: 1.9990 chunk 275 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 chunk 443 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 347 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 613 GLN B 965 GLN A 317 ASN A 505 HIS A 613 GLN A 616 ASN ** J 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** L 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 965 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.090488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.056324 restraints weight = 129100.900| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 4.63 r_work: 0.2888 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 35868 Z= 0.316 Angle : 0.710 11.825 48891 Z= 0.366 Chirality : 0.049 0.296 5484 Planarity : 0.005 0.088 6288 Dihedral : 5.421 59.142 4873 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.45 % Favored : 92.51 % Rotamer: Outliers : 1.64 % Allowed : 12.21 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.12), residues: 4470 helix: 1.65 (0.20), residues: 687 sheet: 0.01 (0.14), residues: 1172 loop : -1.47 (0.12), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 328 TYR 0.039 0.002 TYR A 904 PHE 0.023 0.002 PHE A 592 TRP 0.030 0.002 TRP H 112 HIS 0.010 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00717 (35814) covalent geometry : angle 0.70924 (48783) SS BOND : bond 0.00415 ( 54) SS BOND : angle 1.08495 ( 108) hydrogen bonds : bond 0.04663 ( 1233) hydrogen bonds : angle 5.54854 ( 3423) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 210 time to evaluate : 1.442 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: B 313 TYR cc_start: 0.6314 (OUTLIER) cc_final: 0.6000 (t80) REVERT: B 321 GLN cc_start: 0.8561 (tp40) cc_final: 0.8001 (tp40) REVERT: B 988 GLU cc_start: 0.9027 (mp0) cc_final: 0.8616 (mp0) REVERT: A 321 GLN cc_start: 0.8447 (tp40) cc_final: 0.8131 (tp40) REVERT: A 501 TYR cc_start: 0.5319 (OUTLIER) cc_final: 0.4632 (m-80) REVERT: A 516 GLU cc_start: 0.8447 (tp30) cc_final: 0.8147 (tp30) REVERT: A 546 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8737 (pt) REVERT: A 837 TYR cc_start: 0.8213 (t80) cc_final: 0.7832 (t80) REVERT: J 66 LYS cc_start: 0.8907 (mttp) cc_final: 0.8523 (mmtt) REVERT: G 2 MET cc_start: 0.4840 (tmm) cc_final: 0.4226 (tmm) REVERT: G 53 MET cc_start: 0.5616 (ptp) cc_final: 0.5260 (mpp) REVERT: G 66 ARG cc_start: 0.8257 (tpp80) cc_final: 0.7827 (tmm160) REVERT: H 43 ARG cc_start: 0.8076 (ttm110) cc_final: 0.7218 (ttm-80) REVERT: H 81 ASP cc_start: 0.5405 (OUTLIER) cc_final: 0.4805 (p0) REVERT: L 53 MET cc_start: 0.8164 (mmm) cc_final: 0.7778 (mmm) REVERT: I 11 GLU cc_start: 0.6617 (mm-30) cc_final: 0.6047 (mm-30) REVERT: C 153 MET cc_start: 0.8770 (pmm) cc_final: 0.8458 (pmm) REVERT: C 365 TYR cc_start: 0.9317 (m-80) cc_final: 0.9032 (m-80) REVERT: C 462 LYS cc_start: 0.9579 (mttm) cc_final: 0.9176 (mptt) outliers start: 64 outliers final: 50 residues processed: 262 average time/residue: 0.2384 time to fit residues: 100.7853 Evaluate side-chains 254 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 313 TYR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain J residue 131 LYS Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain K residue 76 PHE Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 170 LYS Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 75 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 401 optimal weight: 0.6980 chunk 298 optimal weight: 10.0000 chunk 430 optimal weight: 1.9990 chunk 230 optimal weight: 0.1980 chunk 20 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 965 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** J 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 205 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 965 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.092218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.058096 restraints weight = 126827.952| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 4.17 r_work: 0.2954 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35868 Z= 0.146 Angle : 0.595 11.866 48891 Z= 0.305 Chirality : 0.045 0.238 5484 Planarity : 0.004 0.075 6288 Dihedral : 5.152 59.726 4873 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.78 % Favored : 93.18 % Rotamer: Outliers : 1.31 % Allowed : 12.85 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.13), residues: 4470 helix: 2.40 (0.21), residues: 636 sheet: 0.04 (0.15), residues: 1121 loop : -1.34 (0.12), residues: 2713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 328 TYR 0.024 0.001 TYR A 904 PHE 0.017 0.001 PHE I 71 TRP 0.027 0.001 TRP I 112 HIS 0.005 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00331 (35814) covalent geometry : angle 0.59405 (48783) SS BOND : bond 0.00269 ( 54) SS BOND : angle 0.80742 ( 108) hydrogen bonds : bond 0.03799 ( 1233) hydrogen bonds : angle 5.24966 ( 3423) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12461.02 seconds wall clock time: 213 minutes 15.60 seconds (12795.60 seconds total)