Starting phenix.real_space_refine on Sun Jun 22 08:57:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqu_34035/06_2025/7yqu_34035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqu_34035/06_2025/7yqu_34035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yqu_34035/06_2025/7yqu_34035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqu_34035/06_2025/7yqu_34035.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqu_34035/06_2025/7yqu_34035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqu_34035/06_2025/7yqu_34035.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.103 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 114 5.16 5 C 16305 2.51 5 N 4209 2.21 5 O 4959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25587 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 1006} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 1006} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 1006} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 14.40, per 1000 atoms: 0.56 Number of scatterers: 25587 At special positions: 0 Unit cell: (143.38, 151.94, 173.34, 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 114 16.00 O 4959 8.00 N 4209 7.00 C 16305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 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 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 B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG A1312 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C1134 " " NAG D 1 " - " ASN C 717 " " NAG E 1 " - " ASN C 801 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " Time building additional restraints: 6.32 Conformation dependent library (CDL) restraints added in 3.3 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5970 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 21.3% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.790A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 371' Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.765A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.695A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.930A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 822 removed outlier: 3.884A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 817 through 822' Processing helix chain 'C' and resid 840 through 844 removed outlier: 3.687A pdb=" N ASP C 843 " --> pdb=" O CYS C 840 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 840 through 844' Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 869 through 880 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.514A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.581A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 937 " --> pdb=" O LYS C 933 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 938 " --> pdb=" O ILE C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.638A pdb=" N ASP C 950 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.699A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.790A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 371' Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.765A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.694A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.930A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 819 Processing helix chain 'A' and resid 820 through 825 Processing helix chain 'A' and resid 840 through 844 removed outlier: 3.687A pdb=" N ASP A 843 " --> pdb=" O CYS A 840 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 840 through 844' Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 869 through 880 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.514A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.581A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.638A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.699A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.790A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 371' Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.766A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.694A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.930A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 822 removed outlier: 3.660A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 844 removed outlier: 3.687A pdb=" N ASP B 843 " --> pdb=" O CYS B 840 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 840 through 844' Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 869 through 880 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.514A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.581A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 965 removed outlier: 3.637A pdb=" N ASP B 950 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.698A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 26 through 30 removed outlier: 7.953A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.537A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.755A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 107 removed outlier: 3.679A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 116 through 118 removed outlier: 3.849A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.318A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.711A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE C 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.787A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.593A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.244A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.783A pdb=" N ALA C 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AB5, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.961A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.645A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.952A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.536A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.755A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 101 through 107 removed outlier: 3.680A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.848A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.318A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.788A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.594A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.244A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AD3, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.961A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.646A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AD6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.953A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 229 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.755A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 101 through 107 removed outlier: 3.679A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.849A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.318A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.788A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.593A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.244A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AE9, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.961A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.645A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'B' and resid 1094 through 1097 802 hydrogen bonds defined for protein. 2193 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: 11.95 Time building geometry restraints manager: 7.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4141 1.31 - 1.44: 7343 1.44 - 1.57: 14553 1.57 - 1.70: 0 1.70 - 1.82: 141 Bond restraints: 26178 Sorted by residual: bond pdb=" N PRO C 373 " pdb=" CA PRO C 373 " ideal model delta sigma weight residual 1.469 1.435 0.034 7.40e-03 1.83e+04 2.10e+01 bond pdb=" C PRO A 373 " pdb=" O PRO A 373 " ideal model delta sigma weight residual 1.235 1.184 0.051 1.30e-02 5.92e+03 1.57e+01 bond pdb=" C PRO B 373 " pdb=" O PRO B 373 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.30e-02 5.92e+03 1.38e+01 bond pdb=" CA ALA C 372 " pdb=" CB ALA C 372 " ideal model delta sigma weight residual 1.530 1.471 0.058 1.58e-02 4.01e+03 1.36e+01 bond pdb=" N PRO B 373 " pdb=" CA PRO B 373 " ideal model delta sigma weight residual 1.469 1.423 0.045 1.28e-02 6.10e+03 1.26e+01 ... (remaining 26173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 35532 4.24 - 8.49: 97 8.49 - 12.73: 6 12.73 - 16.98: 0 16.98 - 21.22: 2 Bond angle restraints: 35637 Sorted by residual: angle pdb=" C PHE B 377 " pdb=" CA PHE B 377 " pdb=" CB PHE B 377 " ideal model delta sigma weight residual 110.79 89.57 21.22 1.63e+00 3.76e-01 1.70e+02 angle pdb=" C PHE C 377 " pdb=" CA PHE C 377 " pdb=" CB PHE C 377 " ideal model delta sigma weight residual 111.68 90.93 20.75 1.68e+00 3.54e-01 1.53e+02 angle pdb=" CA PHE B 377 " pdb=" CB PHE B 377 " pdb=" CG PHE B 377 " ideal model delta sigma weight residual 113.80 122.65 -8.85 1.00e+00 1.00e+00 7.83e+01 angle pdb=" CA PHE C 377 " pdb=" CB PHE C 377 " pdb=" CG PHE C 377 " ideal model delta sigma weight residual 113.80 122.37 -8.57 1.00e+00 1.00e+00 7.34e+01 angle pdb=" C PHE A 377 " pdb=" CA PHE A 377 " pdb=" CB PHE A 377 " ideal model delta sigma weight residual 109.80 97.27 12.53 1.64e+00 3.72e-01 5.84e+01 ... (remaining 35632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14602 17.99 - 35.99: 1300 35.99 - 53.98: 256 53.98 - 71.97: 33 71.97 - 89.97: 36 Dihedral angle restraints: 16227 sinusoidal: 6939 harmonic: 9288 Sorted by residual: dihedral pdb=" C PHE B 377 " pdb=" N PHE B 377 " pdb=" CA PHE B 377 " pdb=" CB PHE B 377 " ideal model delta harmonic sigma weight residual -122.60 -97.22 -25.38 0 2.50e+00 1.60e-01 1.03e+02 dihedral pdb=" C PHE C 377 " pdb=" N PHE C 377 " pdb=" CA PHE C 377 " pdb=" CB PHE C 377 " ideal model delta harmonic sigma weight residual -122.60 -99.91 -22.69 0 2.50e+00 1.60e-01 8.24e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 29.30 63.70 1 1.00e+01 1.00e-02 5.35e+01 ... (remaining 16224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3837 0.092 - 0.185: 321 0.185 - 0.277: 3 0.277 - 0.370: 3 0.370 - 0.462: 3 Chirality restraints: 4167 Sorted by residual: chirality pdb=" CA PHE B 377 " pdb=" N PHE B 377 " pdb=" C PHE B 377 " pdb=" CB PHE B 377 " both_signs ideal model delta sigma weight residual False 2.51 2.97 -0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" CA PHE A 377 " pdb=" N PHE A 377 " pdb=" C PHE A 377 " pdb=" CB PHE A 377 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA PHE C 377 " pdb=" N PHE C 377 " pdb=" C PHE C 377 " pdb=" CB PHE C 377 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.85e+00 ... (remaining 4164 not shown) Planarity restraints: 4605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 372 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C ALA A 372 " -0.073 2.00e-02 2.50e+03 pdb=" O ALA A 372 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO A 373 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 372 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ALA B 372 " 0.066 2.00e-02 2.50e+03 pdb=" O ALA B 372 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO B 373 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 818 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C ILE C 818 " -0.064 2.00e-02 2.50e+03 pdb=" O ILE C 818 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU C 819 " 0.022 2.00e-02 2.50e+03 ... (remaining 4602 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 3 2.12 - 2.81: 7558 2.81 - 3.51: 30387 3.51 - 4.20: 53037 4.20 - 4.90: 99490 Nonbonded interactions: 190475 Sorted by model distance: nonbonded pdb=" NH2 ARG C 847 " pdb=" OD2 ASP A 568 " model vdw 1.425 3.120 nonbonded pdb=" NH2 ARG A 847 " pdb=" OD2 ASP B 568 " model vdw 1.443 3.120 nonbonded pdb=" OD2 ASP C 568 " pdb=" NH2 ARG B 847 " model vdw 1.445 3.120 nonbonded pdb=" CG1 VAL C1094 " pdb=" OH TYR B 904 " model vdw 2.160 3.460 nonbonded pdb=" OH TYR A 904 " pdb=" CG1 VAL B1094 " model vdw 2.180 3.460 ... (remaining 190470 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 57.460 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.140 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 0.005 0.058 26265 Z= 0.241 Angle : 0.737 21.223 35859 Z= 0.396 Chirality : 0.050 0.462 4167 Planarity : 0.004 0.042 4563 Dihedral : 14.037 89.966 10140 Min Nonbonded Distance : 1.425 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.48 % Favored : 91.48 % Rotamer: Outliers : 0.14 % Allowed : 0.22 % Favored : 99.64 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3159 helix: 0.28 (0.22), residues: 609 sheet: 0.29 (0.20), residues: 630 loop : -1.95 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 64 HIS 0.003 0.001 HIS C1064 PHE 0.028 0.002 PHE A 906 TYR 0.047 0.002 TYR A 495 ARG 0.005 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 42) link_NAG-ASN : angle 2.72564 ( 126) link_BETA1-4 : bond 0.00661 ( 6) link_BETA1-4 : angle 0.98911 ( 18) hydrogen bonds : bond 0.15713 ( 802) hydrogen bonds : angle 6.84116 ( 2193) SS BOND : bond 0.00366 ( 39) SS BOND : angle 1.73186 ( 78) covalent geometry : bond 0.00510 (26178) covalent geometry : angle 0.71640 (35637) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 2.555 Fit side-chains REVERT: C 375 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: C 934 ILE cc_start: 0.9094 (tt) cc_final: 0.8893 (tt) REVERT: C 1050 MET cc_start: 0.8291 (mtp) cc_final: 0.8057 (mtp) REVERT: A 375 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: A 1138 TYR cc_start: 0.7551 (m-80) cc_final: 0.7269 (t80) REVERT: B 375 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: B 428 ASP cc_start: 0.7994 (p0) cc_final: 0.7749 (p0) REVERT: B 985 ASP cc_start: 0.8294 (p0) cc_final: 0.7995 (p0) REVERT: B 1072 GLU cc_start: 0.8106 (pm20) cc_final: 0.7783 (pm20) outliers start: 4 outliers final: 0 residues processed: 212 average time/residue: 0.3702 time to fit residues: 126.4784 Evaluate side-chains 166 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 375 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.9980 chunk 241 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 162 optimal weight: 0.0570 chunk 128 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 288 optimal weight: 9.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN A 134 GLN A 207 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.093674 restraints weight = 35510.463| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.82 r_work: 0.2916 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26265 Z= 0.159 Angle : 0.622 12.270 35859 Z= 0.311 Chirality : 0.046 0.330 4167 Planarity : 0.005 0.068 4563 Dihedral : 6.363 56.911 4440 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.79 % Allowed : 6.42 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 3159 helix: 0.64 (0.22), residues: 615 sheet: 0.50 (0.20), residues: 660 loop : -2.01 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.004 0.001 HIS C1064 PHE 0.015 0.001 PHE C 906 TYR 0.037 0.001 TYR C 495 ARG 0.002 0.000 ARG A 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 42) link_NAG-ASN : angle 2.72297 ( 126) link_BETA1-4 : bond 0.00328 ( 6) link_BETA1-4 : angle 0.99645 ( 18) hydrogen bonds : bond 0.05954 ( 802) hydrogen bonds : angle 5.29743 ( 2193) SS BOND : bond 0.00290 ( 39) SS BOND : angle 1.39701 ( 78) covalent geometry : bond 0.00380 (26178) covalent geometry : angle 0.59815 (35637) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 2.621 Fit side-chains REVERT: C 375 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: C 1072 GLU cc_start: 0.8643 (pm20) cc_final: 0.8353 (pm20) REVERT: A 134 GLN cc_start: 0.6919 (tm130) cc_final: 0.6624 (tm-30) REVERT: A 1138 TYR cc_start: 0.7762 (m-80) cc_final: 0.7012 (t80) REVERT: B 375 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: B 377 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7372 (m-10) REVERT: B 1072 GLU cc_start: 0.8647 (pm20) cc_final: 0.8288 (pm20) outliers start: 22 outliers final: 16 residues processed: 171 average time/residue: 0.3596 time to fit residues: 100.0970 Evaluate side-chains 168 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 973 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 42 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 220 optimal weight: 0.9990 chunk 295 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN C 506 GLN A 207 HIS A 506 GLN A1125 ASN B 134 GLN B 207 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.126073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.094339 restraints weight = 35404.577| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.82 r_work: 0.2928 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26265 Z= 0.130 Angle : 0.576 12.198 35859 Z= 0.286 Chirality : 0.045 0.341 4167 Planarity : 0.004 0.059 4563 Dihedral : 5.682 56.552 4440 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.15 % Allowed : 8.73 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 3159 helix: 0.90 (0.23), residues: 612 sheet: 0.58 (0.20), residues: 660 loop : -1.94 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS A 207 PHE 0.016 0.001 PHE B 906 TYR 0.030 0.001 TYR A 495 ARG 0.002 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 42) link_NAG-ASN : angle 2.70223 ( 126) link_BETA1-4 : bond 0.00405 ( 6) link_BETA1-4 : angle 0.93392 ( 18) hydrogen bonds : bond 0.05261 ( 802) hydrogen bonds : angle 5.00368 ( 2193) SS BOND : bond 0.00211 ( 39) SS BOND : angle 1.18436 ( 78) covalent geometry : bond 0.00306 (26178) covalent geometry : angle 0.55180 (35637) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 2.790 Fit side-chains REVERT: C 375 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7886 (m-80) REVERT: C 1072 GLU cc_start: 0.8649 (pm20) cc_final: 0.8376 (pm20) REVERT: A 134 GLN cc_start: 0.7037 (tm130) cc_final: 0.6501 (tm-30) REVERT: A 574 ASP cc_start: 0.8615 (t0) cc_final: 0.8115 (t0) REVERT: A 1138 TYR cc_start: 0.7645 (m-80) cc_final: 0.6961 (t80) REVERT: B 134 GLN cc_start: 0.6937 (tm130) cc_final: 0.6728 (tm-30) REVERT: B 375 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7924 (m-80) REVERT: B 1072 GLU cc_start: 0.8640 (pm20) cc_final: 0.8283 (pm20) outliers start: 32 outliers final: 20 residues processed: 195 average time/residue: 0.3615 time to fit residues: 115.9773 Evaluate side-chains 179 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 241 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 297 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 264 optimal weight: 0.8980 chunk 229 optimal weight: 10.0000 chunk 317 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN A 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.094320 restraints weight = 35562.783| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.83 r_work: 0.2934 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26265 Z= 0.122 Angle : 0.559 11.870 35859 Z= 0.278 Chirality : 0.045 0.340 4167 Planarity : 0.004 0.055 4563 Dihedral : 5.248 56.567 4438 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.55 % Allowed : 9.74 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.15), residues: 3159 helix: 0.97 (0.23), residues: 615 sheet: 0.66 (0.20), residues: 660 loop : -1.92 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.004 0.000 HIS A 207 PHE 0.015 0.001 PHE C 906 TYR 0.024 0.001 TYR C 495 ARG 0.002 0.000 ARG C 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 42) link_NAG-ASN : angle 2.63470 ( 126) link_BETA1-4 : bond 0.00406 ( 6) link_BETA1-4 : angle 0.93933 ( 18) hydrogen bonds : bond 0.04999 ( 802) hydrogen bonds : angle 4.85529 ( 2193) SS BOND : bond 0.00200 ( 39) SS BOND : angle 1.05573 ( 78) covalent geometry : bond 0.00285 (26178) covalent geometry : angle 0.53586 (35637) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 2.587 Fit side-chains REVERT: C 212 LEU cc_start: 0.3896 (OUTLIER) cc_final: 0.3616 (tp) REVERT: C 375 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: C 495 TYR cc_start: 0.7642 (OUTLIER) cc_final: 0.5603 (t80) REVERT: C 1072 GLU cc_start: 0.8694 (pm20) cc_final: 0.8452 (pm20) REVERT: A 134 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6353 (tm-30) REVERT: A 212 LEU cc_start: 0.4314 (OUTLIER) cc_final: 0.3844 (tp) REVERT: A 495 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.6978 (t80) REVERT: A 574 ASP cc_start: 0.8591 (t0) cc_final: 0.8106 (t0) REVERT: A 1138 TYR cc_start: 0.7479 (m-80) cc_final: 0.7032 (t80) REVERT: B 134 GLN cc_start: 0.6939 (tm130) cc_final: 0.6597 (tm-30) REVERT: B 212 LEU cc_start: 0.4318 (OUTLIER) cc_final: 0.3999 (tp) REVERT: B 375 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: B 495 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.6333 (t80) REVERT: B 900 MET cc_start: 0.8978 (mtp) cc_final: 0.8768 (mtm) REVERT: B 1072 GLU cc_start: 0.8661 (pm20) cc_final: 0.8294 (pm20) outliers start: 43 outliers final: 23 residues processed: 205 average time/residue: 0.3359 time to fit residues: 115.2488 Evaluate side-chains 194 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 213 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 283 optimal weight: 0.1980 chunk 188 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 233 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 59 optimal weight: 0.0040 chunk 147 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN A 207 HIS A1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.130679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.098605 restraints weight = 35642.834| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.94 r_work: 0.2985 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 26265 Z= 0.088 Angle : 0.514 11.384 35859 Z= 0.255 Chirality : 0.044 0.327 4167 Planarity : 0.004 0.051 4563 Dihedral : 4.765 56.610 4438 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.41 % Allowed : 11.18 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3159 helix: 1.09 (0.23), residues: 621 sheet: 0.58 (0.21), residues: 633 loop : -1.73 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.004 0.000 HIS A 207 PHE 0.010 0.001 PHE A 133 TYR 0.017 0.001 TYR C1138 ARG 0.002 0.000 ARG C 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 42) link_NAG-ASN : angle 2.47948 ( 126) link_BETA1-4 : bond 0.00411 ( 6) link_BETA1-4 : angle 0.93571 ( 18) hydrogen bonds : bond 0.03935 ( 802) hydrogen bonds : angle 4.61696 ( 2193) SS BOND : bond 0.00147 ( 39) SS BOND : angle 0.74682 ( 78) covalent geometry : bond 0.00183 (26178) covalent geometry : angle 0.49253 (35637) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 3.057 Fit side-chains REVERT: C 212 LEU cc_start: 0.3599 (OUTLIER) cc_final: 0.3338 (tp) REVERT: C 375 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: C 495 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.5490 (t80) REVERT: C 902 MET cc_start: 0.9025 (tpp) cc_final: 0.8655 (mmm) REVERT: A 134 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.6322 (tm-30) REVERT: A 212 LEU cc_start: 0.3950 (OUTLIER) cc_final: 0.3593 (tp) REVERT: A 574 ASP cc_start: 0.8504 (t0) cc_final: 0.8034 (t0) REVERT: A 1138 TYR cc_start: 0.7459 (m-80) cc_final: 0.6998 (t80) REVERT: B 134 GLN cc_start: 0.6874 (tm130) cc_final: 0.6466 (tm-30) REVERT: B 212 LEU cc_start: 0.4127 (OUTLIER) cc_final: 0.3790 (tp) REVERT: B 495 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.5982 (t80) REVERT: B 649 CYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8216 (p) REVERT: B 1072 GLU cc_start: 0.8695 (pm20) cc_final: 0.8382 (pm20) outliers start: 39 outliers final: 23 residues processed: 210 average time/residue: 0.3399 time to fit residues: 120.0791 Evaluate side-chains 197 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 96 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 284 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 241 optimal weight: 0.1980 chunk 137 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN A 207 HIS A 211 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.098091 restraints weight = 35334.714| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.92 r_work: 0.2978 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 26265 Z= 0.095 Angle : 0.517 10.936 35859 Z= 0.256 Chirality : 0.044 0.329 4167 Planarity : 0.004 0.049 4563 Dihedral : 4.603 56.445 4436 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.52 % Allowed : 12.23 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.15), residues: 3159 helix: 1.14 (0.23), residues: 621 sheet: 0.66 (0.22), residues: 582 loop : -1.71 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.004 0.000 HIS A 207 PHE 0.011 0.001 PHE C 135 TYR 0.017 0.001 TYR C 495 ARG 0.001 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 42) link_NAG-ASN : angle 2.38174 ( 126) link_BETA1-4 : bond 0.00408 ( 6) link_BETA1-4 : angle 0.92621 ( 18) hydrogen bonds : bond 0.04103 ( 802) hydrogen bonds : angle 4.54426 ( 2193) SS BOND : bond 0.00151 ( 39) SS BOND : angle 0.75087 ( 78) covalent geometry : bond 0.00208 (26178) covalent geometry : angle 0.49693 (35637) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 2.711 Fit side-chains REVERT: C 212 LEU cc_start: 0.3527 (OUTLIER) cc_final: 0.3278 (tp) REVERT: C 375 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: C 495 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.5266 (t80) REVERT: C 902 MET cc_start: 0.9034 (tpp) cc_final: 0.8618 (mmm) REVERT: C 933 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8483 (ttpt) REVERT: A 134 GLN cc_start: 0.6723 (OUTLIER) cc_final: 0.6237 (tm-30) REVERT: A 212 LEU cc_start: 0.4268 (OUTLIER) cc_final: 0.3814 (tp) REVERT: A 574 ASP cc_start: 0.8484 (t0) cc_final: 0.8013 (t0) REVERT: A 1138 TYR cc_start: 0.7480 (m-80) cc_final: 0.6990 (t80) REVERT: B 134 GLN cc_start: 0.6865 (tm130) cc_final: 0.6411 (tm-30) REVERT: B 212 LEU cc_start: 0.4246 (OUTLIER) cc_final: 0.3911 (tp) REVERT: B 495 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.6029 (t80) REVERT: B 1072 GLU cc_start: 0.8703 (pm20) cc_final: 0.8390 (pm20) outliers start: 42 outliers final: 28 residues processed: 210 average time/residue: 0.3351 time to fit residues: 117.1929 Evaluate side-chains 203 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 114 optimal weight: 7.9990 chunk 186 optimal weight: 0.6980 chunk 274 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 298 optimal weight: 4.9990 chunk 208 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.127941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.095696 restraints weight = 35763.434| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.93 r_work: 0.2936 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26265 Z= 0.128 Angle : 0.548 10.729 35859 Z= 0.273 Chirality : 0.045 0.326 4167 Planarity : 0.004 0.050 4563 Dihedral : 4.691 56.463 4436 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.62 % Allowed : 12.77 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3159 helix: 1.32 (0.23), residues: 597 sheet: 0.75 (0.20), residues: 684 loop : -1.82 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 633 HIS 0.003 0.000 HIS A 207 PHE 0.014 0.001 PHE A 86 TYR 0.027 0.001 TYR A 495 ARG 0.002 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 42) link_NAG-ASN : angle 2.37977 ( 126) link_BETA1-4 : bond 0.00435 ( 6) link_BETA1-4 : angle 0.91697 ( 18) hydrogen bonds : bond 0.04845 ( 802) hydrogen bonds : angle 4.65350 ( 2193) SS BOND : bond 0.00204 ( 39) SS BOND : angle 0.96546 ( 78) covalent geometry : bond 0.00305 (26178) covalent geometry : angle 0.52840 (35637) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 2.693 Fit side-chains REVERT: C 212 LEU cc_start: 0.3618 (OUTLIER) cc_final: 0.3357 (tp) REVERT: C 375 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: C 495 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.5838 (t80) REVERT: C 933 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8421 (ttpt) REVERT: A 134 GLN cc_start: 0.6749 (OUTLIER) cc_final: 0.6290 (tm-30) REVERT: A 212 LEU cc_start: 0.4151 (OUTLIER) cc_final: 0.3836 (tp) REVERT: A 303 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7324 (pp) REVERT: A 495 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.7100 (t80) REVERT: A 574 ASP cc_start: 0.8514 (t0) cc_final: 0.8117 (t0) REVERT: A 1138 TYR cc_start: 0.7443 (m-80) cc_final: 0.6958 (t80) REVERT: B 134 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.6310 (tm-30) REVERT: B 212 LEU cc_start: 0.4460 (OUTLIER) cc_final: 0.4206 (tp) REVERT: B 495 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.6053 (t80) REVERT: B 1072 GLU cc_start: 0.8723 (pm20) cc_final: 0.8342 (pm20) outliers start: 45 outliers final: 26 residues processed: 200 average time/residue: 0.3345 time to fit residues: 112.9155 Evaluate side-chains 199 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 153 optimal weight: 0.8980 chunk 243 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 chunk 147 optimal weight: 9.9990 chunk 246 optimal weight: 0.0000 chunk 307 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.097487 restraints weight = 35455.478| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.93 r_work: 0.2969 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26265 Z= 0.091 Angle : 0.514 10.346 35859 Z= 0.255 Chirality : 0.044 0.321 4167 Planarity : 0.004 0.049 4563 Dihedral : 4.538 56.558 4436 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.55 % Allowed : 13.06 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 3159 helix: 1.37 (0.23), residues: 603 sheet: 0.62 (0.21), residues: 654 loop : -1.69 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.000 HIS A 207 PHE 0.010 0.001 PHE C 135 TYR 0.017 0.001 TYR A 495 ARG 0.001 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 42) link_NAG-ASN : angle 2.28811 ( 126) link_BETA1-4 : bond 0.00405 ( 6) link_BETA1-4 : angle 0.91653 ( 18) hydrogen bonds : bond 0.04097 ( 802) hydrogen bonds : angle 4.54355 ( 2193) SS BOND : bond 0.00135 ( 39) SS BOND : angle 0.74939 ( 78) covalent geometry : bond 0.00197 (26178) covalent geometry : angle 0.49591 (35637) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 2.850 Fit side-chains REVERT: C 134 GLN cc_start: 0.6672 (tm-30) cc_final: 0.6464 (tm-30) REVERT: C 212 LEU cc_start: 0.3516 (OUTLIER) cc_final: 0.3267 (tp) REVERT: C 375 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8177 (m-80) REVERT: C 495 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.5436 (t80) REVERT: C 646 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8051 (mpp80) REVERT: C 902 MET cc_start: 0.9045 (tpp) cc_final: 0.8608 (mmm) REVERT: A 134 GLN cc_start: 0.6666 (OUTLIER) cc_final: 0.6268 (tm-30) REVERT: A 212 LEU cc_start: 0.4089 (OUTLIER) cc_final: 0.3797 (tp) REVERT: A 574 ASP cc_start: 0.8459 (t0) cc_final: 0.8097 (t0) REVERT: A 1138 TYR cc_start: 0.7571 (m-80) cc_final: 0.7104 (t80) REVERT: B 134 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.6303 (tm-30) REVERT: B 212 LEU cc_start: 0.4541 (OUTLIER) cc_final: 0.4284 (tp) REVERT: B 495 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.6005 (t80) REVERT: B 900 MET cc_start: 0.8880 (mtp) cc_final: 0.8677 (mtm) REVERT: B 1072 GLU cc_start: 0.8694 (pm20) cc_final: 0.8323 (pm20) outliers start: 43 outliers final: 27 residues processed: 201 average time/residue: 0.3377 time to fit residues: 113.3343 Evaluate side-chains 200 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 60 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 284 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 159 optimal weight: 0.0870 chunk 18 optimal weight: 0.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.128311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.096093 restraints weight = 35823.889| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.94 r_work: 0.2942 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26265 Z= 0.119 Angle : 0.542 10.412 35859 Z= 0.268 Chirality : 0.045 0.321 4167 Planarity : 0.004 0.047 4563 Dihedral : 4.597 56.479 4436 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.44 % Allowed : 13.42 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3159 helix: 1.33 (0.23), residues: 603 sheet: 0.62 (0.21), residues: 654 loop : -1.73 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 633 HIS 0.004 0.000 HIS A 207 PHE 0.012 0.001 PHE A 86 TYR 0.024 0.001 TYR C 495 ARG 0.002 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 42) link_NAG-ASN : angle 2.28042 ( 126) link_BETA1-4 : bond 0.00473 ( 6) link_BETA1-4 : angle 0.94187 ( 18) hydrogen bonds : bond 0.04658 ( 802) hydrogen bonds : angle 4.60228 ( 2193) SS BOND : bond 0.00191 ( 39) SS BOND : angle 0.92449 ( 78) covalent geometry : bond 0.00283 (26178) covalent geometry : angle 0.52438 (35637) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 2.904 Fit side-chains REVERT: C 212 LEU cc_start: 0.3608 (OUTLIER) cc_final: 0.3354 (tp) REVERT: C 375 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: C 495 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.6089 (t80) REVERT: C 646 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8060 (mpp80) REVERT: C 1138 TYR cc_start: 0.7242 (t80) cc_final: 0.6938 (t80) REVERT: A 134 GLN cc_start: 0.6648 (OUTLIER) cc_final: 0.6282 (tm-30) REVERT: A 212 LEU cc_start: 0.3970 (OUTLIER) cc_final: 0.3675 (tp) REVERT: A 529 LYS cc_start: 0.7856 (mmmt) cc_final: 0.7370 (mmtp) REVERT: A 574 ASP cc_start: 0.8478 (t0) cc_final: 0.8016 (t0) REVERT: A 1138 TYR cc_start: 0.7542 (m-80) cc_final: 0.7067 (t80) REVERT: B 134 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.6303 (tm-30) REVERT: B 212 LEU cc_start: 0.4645 (OUTLIER) cc_final: 0.4255 (tp) REVERT: B 495 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.6021 (t80) REVERT: B 1072 GLU cc_start: 0.8722 (pm20) cc_final: 0.8403 (pm20) outliers start: 40 outliers final: 26 residues processed: 195 average time/residue: 0.3393 time to fit residues: 111.1239 Evaluate side-chains 194 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 298 optimal weight: 1.9990 chunk 201 optimal weight: 0.0060 chunk 109 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 266 optimal weight: 0.8980 chunk 126 optimal weight: 0.0980 chunk 115 optimal weight: 0.9980 chunk 181 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.129238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.097015 restraints weight = 35703.180| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.95 r_work: 0.2969 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26265 Z= 0.092 Angle : 0.519 9.937 35859 Z= 0.255 Chirality : 0.044 0.317 4167 Planarity : 0.004 0.048 4563 Dihedral : 4.484 56.574 4436 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.33 % Allowed : 13.60 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3159 helix: 1.40 (0.23), residues: 603 sheet: 0.63 (0.21), residues: 654 loop : -1.65 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.000 HIS A 207 PHE 0.010 0.001 PHE C 135 TYR 0.018 0.001 TYR A 495 ARG 0.001 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 42) link_NAG-ASN : angle 2.20608 ( 126) link_BETA1-4 : bond 0.00357 ( 6) link_BETA1-4 : angle 0.90416 ( 18) hydrogen bonds : bond 0.04075 ( 802) hydrogen bonds : angle 4.50969 ( 2193) SS BOND : bond 0.00136 ( 39) SS BOND : angle 0.75026 ( 78) covalent geometry : bond 0.00199 (26178) covalent geometry : angle 0.50210 (35637) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 2.870 Fit side-chains REVERT: C 212 LEU cc_start: 0.3503 (OUTLIER) cc_final: 0.3259 (tp) REVERT: C 375 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: C 495 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.5683 (t80) REVERT: C 646 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8017 (mpp80) REVERT: C 902 MET cc_start: 0.9044 (tpp) cc_final: 0.8598 (mmm) REVERT: C 1138 TYR cc_start: 0.7268 (t80) cc_final: 0.6984 (t80) REVERT: A 134 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.6362 (tm-30) REVERT: A 212 LEU cc_start: 0.3972 (OUTLIER) cc_final: 0.3648 (tp) REVERT: A 529 LYS cc_start: 0.7851 (mmmt) cc_final: 0.7424 (mmtp) REVERT: A 574 ASP cc_start: 0.8434 (t0) cc_final: 0.7985 (t0) REVERT: A 1138 TYR cc_start: 0.7572 (m-80) cc_final: 0.7095 (t80) REVERT: B 134 GLN cc_start: 0.6734 (OUTLIER) cc_final: 0.6241 (tm-30) REVERT: B 212 LEU cc_start: 0.4707 (OUTLIER) cc_final: 0.4283 (tp) REVERT: B 495 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.5971 (t80) REVERT: B 574 ASP cc_start: 0.8631 (t0) cc_final: 0.8396 (t0) REVERT: B 1072 GLU cc_start: 0.8694 (pm20) cc_final: 0.8380 (pm20) outliers start: 37 outliers final: 27 residues processed: 197 average time/residue: 0.3258 time to fit residues: 108.4496 Evaluate side-chains 200 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 91 optimal weight: 1.9990 chunk 192 optimal weight: 0.2980 chunk 240 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 230 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS A 134 GLN A 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.097775 restraints weight = 35433.137| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.93 r_work: 0.2968 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 26265 Z= 0.097 Angle : 0.521 9.706 35859 Z= 0.256 Chirality : 0.044 0.315 4167 Planarity : 0.004 0.047 4563 Dihedral : 4.446 56.479 4436 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.26 % Allowed : 14.11 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 3159 helix: 1.42 (0.23), residues: 603 sheet: 0.70 (0.22), residues: 576 loop : -1.62 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.000 HIS A 207 PHE 0.014 0.001 PHE C 135 TYR 0.020 0.001 TYR C 495 ARG 0.001 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 42) link_NAG-ASN : angle 2.15503 ( 126) link_BETA1-4 : bond 0.00417 ( 6) link_BETA1-4 : angle 0.92049 ( 18) hydrogen bonds : bond 0.04146 ( 802) hydrogen bonds : angle 4.47904 ( 2193) SS BOND : bond 0.00142 ( 39) SS BOND : angle 0.78343 ( 78) covalent geometry : bond 0.00216 (26178) covalent geometry : angle 0.50489 (35637) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10246.41 seconds wall clock time: 177 minutes 32.27 seconds (10652.27 seconds total)