Starting phenix.real_space_refine on Thu Jun 19 15:32:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm1_27523/06_2025/8dm1_27523.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm1_27523/06_2025/8dm1_27523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dm1_27523/06_2025/8dm1_27523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm1_27523/06_2025/8dm1_27523.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm1_27523/06_2025/8dm1_27523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm1_27523/06_2025/8dm1_27523.cif" } resolution = 3.04 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= 0.013 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 101 5.16 5 C 14181 2.51 5 N 3631 2.21 5 O 4363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 22276 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6641 Classifications: {'peptide': 851} Link IDs: {'PTRANS': 43, 'TRANS': 807} Chain breaks: 8 Chain: "B" Number of atoms: 6650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6650 Classifications: {'peptide': 852} Link IDs: {'PTRANS': 43, 'TRANS': 808} Chain breaks: 8 Chain: "C" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8215 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 55, 'TRANS': 992} Chain breaks: 7 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.29, per 1000 atoms: 0.64 Number of scatterers: 22276 At special positions: 0 Unit cell: (138, 149, 173, 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 101 16.00 O 4363 8.00 N 3631 7.00 C 14181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 709 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 122 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 122 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 5.21 Conformation dependent library (CDL) restraints added in 3.0 seconds 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5168 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 41 sheets defined 26.9% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.022A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.598A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.880A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.997A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.145A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.976A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.558A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.698A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.930A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.156A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.044A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.926A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.841A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.564A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 856 removed outlier: 3.730A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.752A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.936A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.052A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.197A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 30 removed outlier: 7.617A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.553A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.015A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.765A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.853A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.740A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.916A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.630A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.460A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.460A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.278A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.676A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 20 through 30 removed outlier: 7.695A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.926A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.849A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.803A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.238A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.827A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.448A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.506A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.506A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.318A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'C' and resid 20 through 30 removed outlier: 7.645A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.999A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.866A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.967A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.909A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.909A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.746A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.957A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.478A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.478A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.431A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 1032 hydrogen bonds defined for protein. 2868 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.90 Time building geometry restraints manager: 6.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6879 1.34 - 1.46: 5361 1.46 - 1.58: 10384 1.58 - 1.70: 0 1.70 - 1.82: 131 Bond restraints: 22755 Sorted by residual: bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.335 1.417 -0.082 1.38e-02 5.25e+03 3.56e+01 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.39e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.10e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.87e+00 ... (remaining 22750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 29929 2.17 - 4.33: 953 4.33 - 6.50: 44 6.50 - 8.67: 23 8.67 - 10.83: 1 Bond angle restraints: 30950 Sorted by residual: angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 122.46 129.76 -7.30 1.41e+00 5.03e-01 2.68e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 122.46 129.55 -7.09 1.41e+00 5.03e-01 2.53e+01 angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 122.46 129.42 -6.96 1.41e+00 5.03e-01 2.44e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 115.96 -5.26 1.22e+00 6.72e-01 1.86e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.93 -5.23 1.22e+00 6.72e-01 1.84e+01 ... (remaining 30945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 13181 17.92 - 35.83: 850 35.83 - 53.75: 200 53.75 - 71.67: 58 71.67 - 89.58: 23 Dihedral angle restraints: 14312 sinusoidal: 6305 harmonic: 8007 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -55.09 -30.91 1 1.00e+01 1.00e-02 1.36e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 -55.46 -30.54 1 1.00e+01 1.00e-02 1.33e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -56.42 -29.58 1 1.00e+01 1.00e-02 1.25e+01 ... (remaining 14309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2471 0.047 - 0.095: 806 0.095 - 0.142: 362 0.142 - 0.189: 56 0.189 - 0.237: 8 Chirality restraints: 3703 Sorted by residual: chirality pdb=" CA ASP A 198 " pdb=" N ASP A 198 " pdb=" C ASP A 198 " pdb=" CB ASP A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB VAL B 227 " pdb=" CA VAL B 227 " pdb=" CG1 VAL B 227 " pdb=" CG2 VAL B 227 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ASP B 198 " pdb=" N ASP B 198 " pdb=" C ASP B 198 " pdb=" CB ASP B 198 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3700 not shown) Planarity restraints: 3957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 953 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C ASN C 953 " -0.066 2.00e-02 2.50e+03 pdb=" O ASN C 953 " 0.025 2.00e-02 2.50e+03 pdb=" N HIS C 954 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 952 " -0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C VAL B 952 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL B 952 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN B 953 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 954 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C HIS B 954 " -0.064 2.00e-02 2.50e+03 pdb=" O HIS B 954 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN B 955 " 0.022 2.00e-02 2.50e+03 ... (remaining 3954 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6584 2.82 - 3.34: 19060 3.34 - 3.86: 38323 3.86 - 4.38: 43747 4.38 - 4.90: 75829 Nonbonded interactions: 183543 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.332 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.335 3.040 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.354 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.360 3.040 ... (remaining 183538 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 528 or resid 530 through 1147 or resid 1301 thr \ ough 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 4.770 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: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 53.350 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 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 0.082 22844 Z= 0.256 Angle : 0.853 10.833 31183 Z= 0.470 Chirality : 0.056 0.237 3703 Planarity : 0.007 0.067 3920 Dihedral : 13.213 89.584 9042 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.54 % Allowed : 4.22 % Favored : 95.24 % 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: 0.41 (0.15), residues: 2699 helix: 1.91 (0.18), residues: 653 sheet: 0.66 (0.19), residues: 611 loop : -0.68 (0.15), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 64 HIS 0.018 0.002 HIS C 954 PHE 0.027 0.002 PHE C 371 TYR 0.032 0.002 TYR C1067 ARG 0.016 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 37) link_NAG-ASN : angle 2.51792 ( 111) link_BETA1-4 : bond 0.00650 ( 18) link_BETA1-4 : angle 1.54008 ( 54) hydrogen bonds : bond 0.11714 ( 985) hydrogen bonds : angle 7.20150 ( 2868) SS BOND : bond 0.00309 ( 34) SS BOND : angle 1.46389 ( 68) covalent geometry : bond 0.00530 (22755) covalent geometry : angle 0.83752 (30950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 558 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8202 (t) cc_final: 0.7581 (p) REVERT: A 137 ASN cc_start: 0.7473 (m110) cc_final: 0.6782 (p0) REVERT: A 201 PHE cc_start: 0.7456 (t80) cc_final: 0.7053 (t80) REVERT: A 615 VAL cc_start: 0.7793 (t) cc_final: 0.7572 (t) REVERT: A 858 LEU cc_start: 0.8335 (mt) cc_final: 0.8115 (mt) REVERT: B 55 PHE cc_start: 0.8208 (m-80) cc_final: 0.7671 (m-80) REVERT: B 177 MET cc_start: 0.7796 (pmm) cc_final: 0.7350 (pmm) REVERT: B 200 TYR cc_start: 0.8266 (m-80) cc_final: 0.7829 (m-80) REVERT: B 202 LYS cc_start: 0.8478 (mttm) cc_final: 0.8004 (mppt) REVERT: B 223 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6196 (mp) REVERT: B 226 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7840 (tp) REVERT: B 330 PRO cc_start: 0.8496 (Cg_exo) cc_final: 0.8003 (Cg_endo) REVERT: B 613 GLN cc_start: 0.8770 (mt0) cc_final: 0.8119 (mp10) REVERT: B 900 MET cc_start: 0.7762 (mtp) cc_final: 0.7457 (mtt) REVERT: B 902 MET cc_start: 0.8866 (tpp) cc_final: 0.8628 (tpt) REVERT: B 917 TYR cc_start: 0.7935 (m-80) cc_final: 0.7522 (m-80) REVERT: B 970 PHE cc_start: 0.8364 (m-80) cc_final: 0.8135 (m-10) REVERT: C 91 TYR cc_start: 0.7359 (t80) cc_final: 0.6899 (t80) REVERT: C 99 ASN cc_start: 0.7971 (p0) cc_final: 0.6938 (t0) REVERT: C 189 LEU cc_start: 0.9391 (tp) cc_final: 0.8578 (tp) REVERT: C 191 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7339 (mp0) REVERT: C 202 LYS cc_start: 0.8072 (mttm) cc_final: 0.7681 (mppt) REVERT: C 220 PHE cc_start: 0.4280 (m-80) cc_final: 0.3868 (m-80) REVERT: C 235 ILE cc_start: 0.6789 (mt) cc_final: 0.6449 (mt) REVERT: C 238 PHE cc_start: 0.5644 (p90) cc_final: 0.5091 (p90) REVERT: C 302 THR cc_start: 0.8788 (m) cc_final: 0.8286 (p) REVERT: C 351 TYR cc_start: 0.8643 (p90) cc_final: 0.8168 (p90) REVERT: C 392 PHE cc_start: 0.6575 (m-80) cc_final: 0.6279 (m-80) REVERT: C 574 ASP cc_start: 0.7487 (t0) cc_final: 0.7200 (t0) REVERT: C 585 LEU cc_start: 0.9024 (mt) cc_final: 0.8607 (mm) outliers start: 13 outliers final: 3 residues processed: 565 average time/residue: 0.3386 time to fit residues: 298.5544 Evaluate side-chains 302 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 297 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 214 optimal weight: 0.0060 chunk 83 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 613 GLN A 710 ASN A 957 GLN B 115 GLN B 245 HIS B 641 ASN B 901 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 926 GLN C1002 GLN C1010 GLN C1011 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.109477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.072235 restraints weight = 52514.740| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.28 r_work: 0.3040 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22844 Z= 0.168 Angle : 0.651 10.801 31183 Z= 0.329 Chirality : 0.048 0.733 3703 Planarity : 0.005 0.067 3920 Dihedral : 7.069 59.735 4096 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.52 % Allowed : 11.63 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.55 (0.15), residues: 2699 helix: 2.04 (0.19), residues: 660 sheet: 0.48 (0.19), residues: 602 loop : -0.46 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 104 HIS 0.006 0.001 HIS C 954 PHE 0.025 0.002 PHE B 823 TYR 0.026 0.002 TYR C 380 ARG 0.007 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 37) link_NAG-ASN : angle 2.41869 ( 111) link_BETA1-4 : bond 0.00328 ( 18) link_BETA1-4 : angle 1.34288 ( 54) hydrogen bonds : bond 0.04264 ( 985) hydrogen bonds : angle 5.71249 ( 2868) SS BOND : bond 0.00298 ( 34) SS BOND : angle 1.26061 ( 68) covalent geometry : bond 0.00365 (22755) covalent geometry : angle 0.63147 (30950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 330 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7774 (m-90) cc_final: 0.7513 (m-10) REVERT: A 137 ASN cc_start: 0.7569 (m110) cc_final: 0.6809 (p0) REVERT: A 177 MET cc_start: 0.6950 (pmm) cc_final: 0.6683 (pmm) REVERT: A 200 TYR cc_start: 0.8018 (m-80) cc_final: 0.7740 (m-80) REVERT: A 201 PHE cc_start: 0.7879 (t80) cc_final: 0.7393 (t80) REVERT: A 314 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8594 (tm-30) REVERT: A 922 LEU cc_start: 0.8921 (tt) cc_final: 0.8708 (tp) REVERT: A 955 ASN cc_start: 0.8262 (m-40) cc_final: 0.7798 (t0) REVERT: A 1021 SER cc_start: 0.9040 (t) cc_final: 0.8803 (t) REVERT: B 55 PHE cc_start: 0.8341 (m-80) cc_final: 0.7556 (m-80) REVERT: B 102 ARG cc_start: 0.6538 (mtm-85) cc_final: 0.6146 (mmm-85) REVERT: B 177 MET cc_start: 0.7442 (pmm) cc_final: 0.7127 (pmm) REVERT: B 330 PRO cc_start: 0.8503 (Cg_exo) cc_final: 0.8205 (Cg_endo) REVERT: B 613 GLN cc_start: 0.9103 (mt0) cc_final: 0.8832 (mp10) REVERT: B 970 PHE cc_start: 0.8710 (m-80) cc_final: 0.8392 (m-80) REVERT: B 979 ASP cc_start: 0.8595 (t0) cc_final: 0.8384 (t0) REVERT: C 99 ASN cc_start: 0.8168 (p0) cc_final: 0.7033 (t0) REVERT: C 189 LEU cc_start: 0.9280 (tp) cc_final: 0.8670 (tp) REVERT: C 191 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7627 (mp0) REVERT: C 235 ILE cc_start: 0.6498 (mt) cc_final: 0.6256 (mt) REVERT: C 238 PHE cc_start: 0.6415 (p90) cc_final: 0.5886 (p90) REVERT: C 302 THR cc_start: 0.8807 (m) cc_final: 0.8591 (p) REVERT: C 351 TYR cc_start: 0.8783 (p90) cc_final: 0.8274 (p90) REVERT: C 353 TRP cc_start: 0.7300 (p-90) cc_final: 0.5382 (p-90) REVERT: C 434 ILE cc_start: 0.3387 (OUTLIER) cc_final: 0.3102 (mt) REVERT: C 498 ARG cc_start: 0.9147 (mtt180) cc_final: 0.8885 (tpp80) REVERT: C 574 ASP cc_start: 0.7920 (t0) cc_final: 0.7607 (t0) REVERT: C 780 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8392 (mt-10) REVERT: C 950 ASP cc_start: 0.8567 (m-30) cc_final: 0.8249 (m-30) REVERT: C 957 GLN cc_start: 0.8481 (tt0) cc_final: 0.8266 (tt0) REVERT: C 994 ASP cc_start: 0.8704 (m-30) cc_final: 0.8440 (m-30) outliers start: 61 outliers final: 31 residues processed: 373 average time/residue: 0.3020 time to fit residues: 184.0016 Evaluate side-chains 288 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 141 optimal weight: 0.0270 chunk 48 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 chunk 223 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 233 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 78 optimal weight: 0.1980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1011 GLN C 66 HIS C 965 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.109605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.072678 restraints weight = 52351.236| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.29 r_work: 0.3028 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22844 Z= 0.121 Angle : 0.555 9.254 31183 Z= 0.283 Chirality : 0.044 0.177 3703 Planarity : 0.004 0.040 3920 Dihedral : 5.988 59.779 4087 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.15 % Allowed : 13.45 % Favored : 84.40 % 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: 0.78 (0.15), residues: 2699 helix: 2.31 (0.20), residues: 665 sheet: 0.51 (0.19), residues: 596 loop : -0.31 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 104 HIS 0.006 0.001 HIS B 954 PHE 0.027 0.001 PHE C 855 TYR 0.023 0.001 TYR A1067 ARG 0.006 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 37) link_NAG-ASN : angle 1.95629 ( 111) link_BETA1-4 : bond 0.00346 ( 18) link_BETA1-4 : angle 1.19020 ( 54) hydrogen bonds : bond 0.03861 ( 985) hydrogen bonds : angle 5.38896 ( 2868) SS BOND : bond 0.00449 ( 34) SS BOND : angle 1.08359 ( 68) covalent geometry : bond 0.00261 (22755) covalent geometry : angle 0.54034 (30950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 279 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7755 (m-90) cc_final: 0.7394 (m-10) REVERT: A 201 PHE cc_start: 0.7980 (t80) cc_final: 0.7449 (t80) REVERT: A 314 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8494 (tm-30) REVERT: A 697 MET cc_start: 0.7834 (ptt) cc_final: 0.7606 (ptt) REVERT: A 866 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8480 (p) REVERT: A 955 ASN cc_start: 0.8279 (m-40) cc_final: 0.7812 (t0) REVERT: A 985 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7142 (p0) REVERT: B 55 PHE cc_start: 0.8133 (m-80) cc_final: 0.7440 (m-80) REVERT: B 102 ARG cc_start: 0.6822 (mtm-85) cc_final: 0.6515 (mmm-85) REVERT: B 177 MET cc_start: 0.7310 (pmm) cc_final: 0.6913 (pmm) REVERT: B 242 LEU cc_start: 0.7926 (mm) cc_final: 0.7612 (mm) REVERT: B 305 SER cc_start: 0.8940 (t) cc_final: 0.8727 (p) REVERT: B 309 GLU cc_start: 0.8911 (mp0) cc_final: 0.8655 (mp0) REVERT: B 330 PRO cc_start: 0.8493 (Cg_exo) cc_final: 0.8200 (Cg_endo) REVERT: B 955 ASN cc_start: 0.8330 (m110) cc_final: 0.7803 (t0) REVERT: B 970 PHE cc_start: 0.8840 (m-80) cc_final: 0.8517 (m-80) REVERT: B 979 ASP cc_start: 0.8536 (t0) cc_final: 0.8327 (t0) REVERT: C 52 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7205 (tp40) REVERT: C 53 ASP cc_start: 0.7032 (t0) cc_final: 0.6738 (t70) REVERT: C 99 ASN cc_start: 0.8145 (p0) cc_final: 0.7011 (t0) REVERT: C 235 ILE cc_start: 0.6442 (mt) cc_final: 0.6199 (mt) REVERT: C 238 PHE cc_start: 0.6493 (p90) cc_final: 0.5933 (p90) REVERT: C 351 TYR cc_start: 0.8788 (p90) cc_final: 0.8249 (p90) REVERT: C 434 ILE cc_start: 0.3615 (OUTLIER) cc_final: 0.3323 (mt) REVERT: C 574 ASP cc_start: 0.7848 (t0) cc_final: 0.7643 (t0) REVERT: C 586 ASP cc_start: 0.7766 (t70) cc_final: 0.7420 (t0) REVERT: C 933 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7811 (mttm) REVERT: C 950 ASP cc_start: 0.8664 (m-30) cc_final: 0.8284 (m-30) REVERT: C 994 ASP cc_start: 0.8672 (m-30) cc_final: 0.8348 (m-30) outliers start: 52 outliers final: 35 residues processed: 313 average time/residue: 0.3418 time to fit residues: 174.4157 Evaluate side-chains 264 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 203 optimal weight: 0.6980 chunk 184 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 173 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 67 optimal weight: 0.3980 chunk 36 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 710 ASN A 762 GLN A 824 ASN A1010 GLN B 23 GLN B 207 HIS ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS C 417 ASN C 824 ASN C 957 GLN C 960 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.107329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.070153 restraints weight = 53705.259| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.26 r_work: 0.2998 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 22844 Z= 0.193 Angle : 0.625 8.283 31183 Z= 0.322 Chirality : 0.046 0.206 3703 Planarity : 0.005 0.073 3920 Dihedral : 5.764 59.795 4087 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.48 % Allowed : 13.07 % Favored : 83.45 % 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: 0.59 (0.16), residues: 2699 helix: 1.85 (0.19), residues: 666 sheet: 0.34 (0.19), residues: 626 loop : -0.25 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 104 HIS 0.007 0.001 HIS B 207 PHE 0.073 0.002 PHE C 855 TYR 0.037 0.002 TYR C 380 ARG 0.005 0.001 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 37) link_NAG-ASN : angle 2.03728 ( 111) link_BETA1-4 : bond 0.00290 ( 18) link_BETA1-4 : angle 1.43120 ( 54) hydrogen bonds : bond 0.04140 ( 985) hydrogen bonds : angle 5.39784 ( 2868) SS BOND : bond 0.00543 ( 34) SS BOND : angle 1.20813 ( 68) covalent geometry : bond 0.00437 (22755) covalent geometry : angle 0.61018 (30950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 233 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7876 (m-90) cc_final: 0.7637 (m-90) REVERT: A 200 TYR cc_start: 0.8197 (m-80) cc_final: 0.7941 (m-80) REVERT: A 201 PHE cc_start: 0.8194 (t80) cc_final: 0.7906 (t80) REVERT: A 314 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8576 (tm-30) REVERT: A 615 VAL cc_start: 0.9322 (OUTLIER) cc_final: 0.9122 (m) REVERT: A 955 ASN cc_start: 0.8617 (m-40) cc_final: 0.8346 (t0) REVERT: A 995 ARG cc_start: 0.9033 (mtp-110) cc_final: 0.8335 (mtp85) REVERT: B 55 PHE cc_start: 0.8012 (m-80) cc_final: 0.7386 (m-80) REVERT: B 104 TRP cc_start: 0.6630 (m-90) cc_final: 0.6424 (m-90) REVERT: B 177 MET cc_start: 0.7330 (pmm) cc_final: 0.6924 (pmm) REVERT: B 202 LYS cc_start: 0.8446 (mttm) cc_final: 0.8176 (mppt) REVERT: B 242 LEU cc_start: 0.8044 (mm) cc_final: 0.7723 (mm) REVERT: B 309 GLU cc_start: 0.9047 (mp0) cc_final: 0.8831 (mp0) REVERT: B 330 PRO cc_start: 0.8633 (Cg_exo) cc_final: 0.8355 (Cg_endo) REVERT: B 731 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8606 (ttp) REVERT: B 1001 LEU cc_start: 0.9169 (tt) cc_final: 0.8868 (tt) REVERT: B 1005 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8429 (mt0) REVERT: B 1117 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.8995 (p) REVERT: C 52 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7800 (tp40) REVERT: C 66 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7329 (t-90) REVERT: C 153 MET cc_start: 0.4316 (pmm) cc_final: 0.4072 (ptp) REVERT: C 177 MET cc_start: 0.6837 (OUTLIER) cc_final: 0.6562 (ptm) REVERT: C 238 PHE cc_start: 0.6912 (p90) cc_final: 0.6458 (p90) REVERT: C 351 TYR cc_start: 0.8775 (p90) cc_final: 0.8267 (p90) REVERT: C 434 ILE cc_start: 0.3934 (OUTLIER) cc_final: 0.3601 (mt) REVERT: C 574 ASP cc_start: 0.7913 (t0) cc_final: 0.7635 (t0) REVERT: C 758 SER cc_start: 0.8739 (OUTLIER) cc_final: 0.8488 (p) REVERT: C 773 GLU cc_start: 0.8651 (tt0) cc_final: 0.8404 (tt0) REVERT: C 900 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8914 (mtm) REVERT: C 933 LYS cc_start: 0.8636 (mmtm) cc_final: 0.8370 (mttm) REVERT: C 950 ASP cc_start: 0.8811 (m-30) cc_final: 0.8344 (m-30) REVERT: C 957 GLN cc_start: 0.8927 (tt0) cc_final: 0.8718 (tt0) REVERT: C 984 LEU cc_start: 0.7907 (tt) cc_final: 0.7655 (tt) outliers start: 84 outliers final: 45 residues processed: 290 average time/residue: 0.3196 time to fit residues: 150.2436 Evaluate side-chains 253 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1018 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 190 optimal weight: 4.9990 chunk 270 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 248 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 824 ASN B 907 ASN B 978 ASN B1002 GLN C 66 HIS C 245 HIS C 394 ASN C 450 ASN C 960 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.105965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.068547 restraints weight = 53228.562| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.32 r_work: 0.2977 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22844 Z= 0.177 Angle : 0.558 10.080 31183 Z= 0.286 Chirality : 0.045 0.192 3703 Planarity : 0.004 0.042 3920 Dihedral : 5.448 58.755 4085 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.65 % Allowed : 14.40 % Favored : 82.95 % 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: 0.67 (0.16), residues: 2699 helix: 2.05 (0.20), residues: 667 sheet: 0.20 (0.19), residues: 636 loop : -0.16 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 258 HIS 0.011 0.001 HIS C 245 PHE 0.025 0.001 PHE B 823 TYR 0.022 0.001 TYR A1067 ARG 0.007 0.000 ARG C1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 37) link_NAG-ASN : angle 1.80701 ( 111) link_BETA1-4 : bond 0.00260 ( 18) link_BETA1-4 : angle 1.11461 ( 54) hydrogen bonds : bond 0.03843 ( 985) hydrogen bonds : angle 5.25307 ( 2868) SS BOND : bond 0.00281 ( 34) SS BOND : angle 1.05875 ( 68) covalent geometry : bond 0.00401 (22755) covalent geometry : angle 0.54544 (30950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 214 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8246 (tm-30) REVERT: A 104 TRP cc_start: 0.7841 (m-90) cc_final: 0.7604 (m-90) REVERT: A 200 TYR cc_start: 0.7996 (m-80) cc_final: 0.7594 (m-80) REVERT: A 201 PHE cc_start: 0.8419 (t80) cc_final: 0.8193 (t80) REVERT: A 214 ARG cc_start: 0.6825 (tpt-90) cc_final: 0.6578 (tpt-90) REVERT: A 314 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8504 (tm-30) REVERT: A 786 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8450 (mmmt) REVERT: A 955 ASN cc_start: 0.8663 (m-40) cc_final: 0.8247 (t0) REVERT: B 55 PHE cc_start: 0.8071 (m-80) cc_final: 0.7437 (m-80) REVERT: B 177 MET cc_start: 0.7398 (pmm) cc_final: 0.6857 (pmm) REVERT: B 202 LYS cc_start: 0.8402 (mttm) cc_final: 0.8155 (mppt) REVERT: B 224 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: B 242 LEU cc_start: 0.8004 (mm) cc_final: 0.7309 (mp) REVERT: B 309 GLU cc_start: 0.9043 (mp0) cc_final: 0.8653 (mp0) REVERT: B 313 TYR cc_start: 0.8967 (m-80) cc_final: 0.8561 (m-80) REVERT: B 330 PRO cc_start: 0.8624 (Cg_exo) cc_final: 0.8342 (Cg_endo) REVERT: B 731 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8740 (mtm) REVERT: B 955 ASN cc_start: 0.8713 (m110) cc_final: 0.8299 (t0) REVERT: B 988 GLU cc_start: 0.9066 (tp30) cc_final: 0.8829 (tp30) REVERT: B 1005 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8669 (mt0) REVERT: C 52 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7701 (tp40) REVERT: C 53 ASP cc_start: 0.7669 (t0) cc_final: 0.7278 (t0) REVERT: C 99 ASN cc_start: 0.8131 (p0) cc_final: 0.7082 (t0) REVERT: C 177 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6188 (ptm) REVERT: C 238 PHE cc_start: 0.7050 (p90) cc_final: 0.6675 (p90) REVERT: C 309 GLU cc_start: 0.8664 (mp0) cc_final: 0.8306 (mp0) REVERT: C 351 TYR cc_start: 0.8828 (p90) cc_final: 0.8397 (p90) REVERT: C 434 ILE cc_start: 0.4185 (OUTLIER) cc_final: 0.3899 (mt) REVERT: C 586 ASP cc_start: 0.7796 (t70) cc_final: 0.7557 (t0) REVERT: C 773 GLU cc_start: 0.8685 (tt0) cc_final: 0.8210 (tt0) REVERT: C 900 MET cc_start: 0.9169 (mtm) cc_final: 0.8907 (mtm) REVERT: C 933 LYS cc_start: 0.8639 (mmtm) cc_final: 0.8414 (mttm) REVERT: C 950 ASP cc_start: 0.8799 (m-30) cc_final: 0.8313 (m-30) REVERT: C 957 GLN cc_start: 0.8922 (tt0) cc_final: 0.8677 (tt0) REVERT: C 984 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7652 (tt) outliers start: 64 outliers final: 41 residues processed: 263 average time/residue: 0.3211 time to fit residues: 136.9429 Evaluate side-chains 238 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1018 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 131 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 223 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 66 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 450 ASN C 960 ASN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.105032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.067654 restraints weight = 52968.936| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.26 r_work: 0.2952 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.6316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22844 Z= 0.195 Angle : 0.573 10.932 31183 Z= 0.295 Chirality : 0.045 0.190 3703 Planarity : 0.004 0.042 3920 Dihedral : 5.410 59.934 4085 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.73 % Allowed : 15.06 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.71 (0.16), residues: 2699 helix: 2.12 (0.20), residues: 667 sheet: 0.16 (0.19), residues: 644 loop : -0.13 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.019 0.001 HIS C 245 PHE 0.033 0.002 PHE B 220 TYR 0.022 0.001 TYR B 170 ARG 0.006 0.000 ARG C 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 37) link_NAG-ASN : angle 1.82065 ( 111) link_BETA1-4 : bond 0.00175 ( 18) link_BETA1-4 : angle 1.10964 ( 54) hydrogen bonds : bond 0.03890 ( 985) hydrogen bonds : angle 5.26835 ( 2868) SS BOND : bond 0.00201 ( 34) SS BOND : angle 1.10863 ( 68) covalent geometry : bond 0.00444 (22755) covalent geometry : angle 0.56012 (30950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 198 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8428 (tm-30) REVERT: A 104 TRP cc_start: 0.7846 (m-90) cc_final: 0.7531 (m-90) REVERT: A 157 PHE cc_start: 0.7821 (m-10) cc_final: 0.7585 (m-10) REVERT: A 200 TYR cc_start: 0.8154 (m-80) cc_final: 0.7815 (m-80) REVERT: A 201 PHE cc_start: 0.8361 (t80) cc_final: 0.8085 (t80) REVERT: A 214 ARG cc_start: 0.7051 (tpt-90) cc_final: 0.6844 (tpt-90) REVERT: A 314 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8476 (tm-30) REVERT: A 866 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8884 (p) REVERT: A 955 ASN cc_start: 0.8688 (m-40) cc_final: 0.8280 (t0) REVERT: B 55 PHE cc_start: 0.8031 (m-80) cc_final: 0.7390 (m-80) REVERT: B 177 MET cc_start: 0.7378 (pmm) cc_final: 0.6785 (pmm) REVERT: B 242 LEU cc_start: 0.8027 (mm) cc_final: 0.7367 (mp) REVERT: B 330 PRO cc_start: 0.8659 (Cg_exo) cc_final: 0.8382 (Cg_endo) REVERT: B 571 ASP cc_start: 0.8549 (m-30) cc_final: 0.8319 (t0) REVERT: B 731 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8830 (mtm) REVERT: B 955 ASN cc_start: 0.8759 (m110) cc_final: 0.8356 (t0) REVERT: B 988 GLU cc_start: 0.9155 (tp30) cc_final: 0.8838 (tp30) REVERT: B 1005 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8640 (mt0) REVERT: C 52 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8099 (tm-30) REVERT: C 238 PHE cc_start: 0.7140 (p90) cc_final: 0.6923 (p90) REVERT: C 309 GLU cc_start: 0.8711 (mp0) cc_final: 0.8360 (mp0) REVERT: C 351 TYR cc_start: 0.8856 (p90) cc_final: 0.8471 (p90) REVERT: C 434 ILE cc_start: 0.4262 (OUTLIER) cc_final: 0.3972 (mt) REVERT: C 773 GLU cc_start: 0.8675 (tt0) cc_final: 0.8263 (tt0) REVERT: C 855 PHE cc_start: 0.8449 (m-80) cc_final: 0.8140 (t80) REVERT: C 900 MET cc_start: 0.9172 (mtm) cc_final: 0.8925 (mtm) REVERT: C 957 GLN cc_start: 0.8947 (tt0) cc_final: 0.8734 (tt0) REVERT: C 984 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7551 (tp) REVERT: C 994 ASP cc_start: 0.8704 (m-30) cc_final: 0.8347 (t70) outliers start: 66 outliers final: 40 residues processed: 249 average time/residue: 0.3202 time to fit residues: 129.1563 Evaluate side-chains 225 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1018 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 83 optimal weight: 0.0070 chunk 195 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 233 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 268 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN C 66 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.106099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.069078 restraints weight = 52966.166| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.25 r_work: 0.2972 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22844 Z= 0.143 Angle : 0.553 11.105 31183 Z= 0.284 Chirality : 0.044 0.185 3703 Planarity : 0.004 0.041 3920 Dihedral : 5.217 59.444 4085 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.40 % Allowed : 15.39 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.80 (0.16), residues: 2699 helix: 2.28 (0.20), residues: 666 sheet: 0.21 (0.18), residues: 650 loop : -0.11 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 104 HIS 0.005 0.001 HIS C 207 PHE 0.024 0.001 PHE B 220 TYR 0.022 0.001 TYR B 170 ARG 0.007 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 37) link_NAG-ASN : angle 1.71255 ( 111) link_BETA1-4 : bond 0.00305 ( 18) link_BETA1-4 : angle 1.00771 ( 54) hydrogen bonds : bond 0.03653 ( 985) hydrogen bonds : angle 5.14549 ( 2868) SS BOND : bond 0.00342 ( 34) SS BOND : angle 1.02036 ( 68) covalent geometry : bond 0.00324 (22755) covalent geometry : angle 0.54153 (30950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 209 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8586 (mm) cc_final: 0.8148 (tp) REVERT: A 52 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8447 (tm-30) REVERT: A 99 ASN cc_start: 0.8359 (m-40) cc_final: 0.7634 (p0) REVERT: A 104 TRP cc_start: 0.7846 (m-90) cc_final: 0.7492 (m-90) REVERT: A 157 PHE cc_start: 0.7797 (m-10) cc_final: 0.7590 (m-10) REVERT: A 173 GLN cc_start: 0.8640 (pm20) cc_final: 0.8425 (mm-40) REVERT: A 200 TYR cc_start: 0.8064 (m-80) cc_final: 0.7520 (m-80) REVERT: A 201 PHE cc_start: 0.8477 (t80) cc_final: 0.8247 (t80) REVERT: A 314 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8434 (tm-30) REVERT: A 955 ASN cc_start: 0.8704 (m-40) cc_final: 0.8287 (t0) REVERT: B 55 PHE cc_start: 0.8195 (m-80) cc_final: 0.7569 (m-80) REVERT: B 177 MET cc_start: 0.7210 (pmm) cc_final: 0.6637 (pmm) REVERT: B 224 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: B 242 LEU cc_start: 0.8018 (mm) cc_final: 0.7407 (mp) REVERT: B 330 PRO cc_start: 0.8609 (Cg_exo) cc_final: 0.8323 (Cg_endo) REVERT: B 571 ASP cc_start: 0.8515 (m-30) cc_final: 0.8234 (t0) REVERT: B 725 GLU cc_start: 0.8922 (tt0) cc_final: 0.8641 (tt0) REVERT: B 731 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8853 (mtm) REVERT: B 759 PHE cc_start: 0.8277 (m-80) cc_final: 0.8070 (m-80) REVERT: B 955 ASN cc_start: 0.8763 (m110) cc_final: 0.8393 (t0) REVERT: B 988 GLU cc_start: 0.9143 (tp30) cc_final: 0.8756 (tp30) REVERT: C 52 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7715 (tp40) REVERT: C 53 ASP cc_start: 0.7627 (t0) cc_final: 0.7139 (t70) REVERT: C 220 PHE cc_start: 0.6504 (t80) cc_final: 0.6290 (t80) REVERT: C 324 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: C 351 TYR cc_start: 0.8876 (p90) cc_final: 0.8507 (p90) REVERT: C 396 TYR cc_start: 0.7446 (m-80) cc_final: 0.6153 (m-80) REVERT: C 434 ILE cc_start: 0.4420 (OUTLIER) cc_final: 0.4134 (mt) REVERT: C 773 GLU cc_start: 0.8681 (tt0) cc_final: 0.8273 (tt0) REVERT: C 900 MET cc_start: 0.9143 (mtm) cc_final: 0.8907 (mtm) REVERT: C 957 GLN cc_start: 0.8924 (tt0) cc_final: 0.8712 (tt0) REVERT: C 984 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7620 (tp) REVERT: C 994 ASP cc_start: 0.8659 (m-30) cc_final: 0.8342 (t70) REVERT: C 1017 GLU cc_start: 0.9170 (tt0) cc_final: 0.8923 (tm-30) outliers start: 58 outliers final: 39 residues processed: 253 average time/residue: 0.3136 time to fit residues: 131.7261 Evaluate side-chains 239 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 270 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 206 optimal weight: 5.9990 chunk 139 optimal weight: 0.3980 chunk 203 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 66 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.105671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.068750 restraints weight = 53116.924| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.30 r_work: 0.2958 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22844 Z= 0.153 Angle : 0.564 12.425 31183 Z= 0.286 Chirality : 0.044 0.175 3703 Planarity : 0.004 0.042 3920 Dihedral : 5.074 58.360 4085 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.32 % Allowed : 15.97 % Favored : 81.71 % 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: 0.84 (0.16), residues: 2699 helix: 2.33 (0.19), residues: 666 sheet: 0.21 (0.19), residues: 649 loop : -0.09 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 104 HIS 0.005 0.001 HIS C 207 PHE 0.023 0.001 PHE B 823 TYR 0.031 0.001 TYR B 170 ARG 0.006 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 37) link_NAG-ASN : angle 1.70482 ( 111) link_BETA1-4 : bond 0.00236 ( 18) link_BETA1-4 : angle 1.05647 ( 54) hydrogen bonds : bond 0.03670 ( 985) hydrogen bonds : angle 5.14012 ( 2868) SS BOND : bond 0.00182 ( 34) SS BOND : angle 1.02451 ( 68) covalent geometry : bond 0.00348 (22755) covalent geometry : angle 0.55309 (30950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8577 (mm) cc_final: 0.8147 (tp) REVERT: A 52 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8438 (tm-30) REVERT: A 99 ASN cc_start: 0.8363 (m-40) cc_final: 0.7637 (p0) REVERT: A 104 TRP cc_start: 0.7864 (m-90) cc_final: 0.7548 (m-90) REVERT: A 200 TYR cc_start: 0.8026 (m-80) cc_final: 0.7631 (m-80) REVERT: A 201 PHE cc_start: 0.8465 (t80) cc_final: 0.8236 (t80) REVERT: A 214 ARG cc_start: 0.6928 (tpt-90) cc_final: 0.6699 (tpt-90) REVERT: A 231 ILE cc_start: 0.9077 (mm) cc_final: 0.8854 (mm) REVERT: A 314 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8406 (tm-30) REVERT: A 955 ASN cc_start: 0.8718 (m-40) cc_final: 0.8302 (t0) REVERT: A 988 GLU cc_start: 0.9072 (mp0) cc_final: 0.8610 (pm20) REVERT: B 55 PHE cc_start: 0.8166 (m-80) cc_final: 0.7560 (m-80) REVERT: B 177 MET cc_start: 0.7120 (pmm) cc_final: 0.6529 (pmm) REVERT: B 223 LEU cc_start: 0.8176 (mp) cc_final: 0.7930 (mt) REVERT: B 224 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: B 242 LEU cc_start: 0.8097 (mm) cc_final: 0.7533 (mp) REVERT: B 269 TYR cc_start: 0.7660 (m-80) cc_final: 0.7380 (m-10) REVERT: B 330 PRO cc_start: 0.8594 (Cg_exo) cc_final: 0.8307 (Cg_endo) REVERT: B 571 ASP cc_start: 0.8529 (m-30) cc_final: 0.8229 (t0) REVERT: B 725 GLU cc_start: 0.8942 (tt0) cc_final: 0.8685 (tt0) REVERT: B 768 THR cc_start: 0.9217 (m) cc_final: 0.8993 (p) REVERT: B 955 ASN cc_start: 0.8740 (m110) cc_final: 0.8391 (t0) REVERT: B 988 GLU cc_start: 0.9176 (tp30) cc_final: 0.8795 (tp30) REVERT: C 52 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8241 (tm-30) REVERT: C 177 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.6458 (ptt) REVERT: C 324 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: C 351 TYR cc_start: 0.8894 (p90) cc_final: 0.8530 (p90) REVERT: C 434 ILE cc_start: 0.4588 (OUTLIER) cc_final: 0.4276 (mt) REVERT: C 756 TYR cc_start: 0.9087 (m-80) cc_final: 0.8839 (m-80) REVERT: C 773 GLU cc_start: 0.8688 (tt0) cc_final: 0.8314 (tt0) REVERT: C 900 MET cc_start: 0.9162 (mtm) cc_final: 0.8902 (mtm) REVERT: C 923 ILE cc_start: 0.9622 (OUTLIER) cc_final: 0.9387 (mp) REVERT: C 950 ASP cc_start: 0.8803 (m-30) cc_final: 0.8300 (m-30) REVERT: C 984 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7606 (tp) REVERT: C 994 ASP cc_start: 0.8657 (m-30) cc_final: 0.8378 (t70) REVERT: C 1017 GLU cc_start: 0.9144 (tt0) cc_final: 0.8943 (tm-30) outliers start: 56 outliers final: 41 residues processed: 249 average time/residue: 0.3139 time to fit residues: 127.7620 Evaluate side-chains 230 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 192 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 212 optimal weight: 9.9990 chunk 230 optimal weight: 0.6980 chunk 56 optimal weight: 0.0020 chunk 86 optimal weight: 0.0470 overall best weight: 0.4686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C 960 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.106888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.070158 restraints weight = 53058.109| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.32 r_work: 0.2990 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22844 Z= 0.110 Angle : 0.552 12.061 31183 Z= 0.280 Chirality : 0.044 0.175 3703 Planarity : 0.004 0.048 3920 Dihedral : 4.918 58.317 4085 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.15 % Allowed : 16.34 % Favored : 81.51 % 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 (0.16), residues: 2699 helix: 2.43 (0.20), residues: 666 sheet: 0.24 (0.19), residues: 643 loop : -0.06 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 353 HIS 0.004 0.001 HIS C 207 PHE 0.023 0.001 PHE B 823 TYR 0.023 0.001 TYR B 170 ARG 0.005 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 37) link_NAG-ASN : angle 1.58211 ( 111) link_BETA1-4 : bond 0.00343 ( 18) link_BETA1-4 : angle 0.95365 ( 54) hydrogen bonds : bond 0.03477 ( 985) hydrogen bonds : angle 5.02926 ( 2868) SS BOND : bond 0.00166 ( 34) SS BOND : angle 0.97122 ( 68) covalent geometry : bond 0.00246 (22755) covalent geometry : angle 0.54240 (30950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 202 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8616 (mm) cc_final: 0.8239 (tp) REVERT: A 52 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8442 (tm-30) REVERT: A 99 ASN cc_start: 0.8341 (m-40) cc_final: 0.7644 (p0) REVERT: A 101 ILE cc_start: 0.8415 (mp) cc_final: 0.8131 (mm) REVERT: A 104 TRP cc_start: 0.7828 (m-90) cc_final: 0.7517 (m-90) REVERT: A 173 GLN cc_start: 0.8538 (pm20) cc_final: 0.8240 (tp40) REVERT: A 200 TYR cc_start: 0.8050 (m-80) cc_final: 0.7686 (m-80) REVERT: A 201 PHE cc_start: 0.8487 (t80) cc_final: 0.8261 (t80) REVERT: A 214 ARG cc_start: 0.6949 (tpt-90) cc_final: 0.6738 (tpt-90) REVERT: A 314 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8393 (tm-30) REVERT: A 955 ASN cc_start: 0.8712 (m-40) cc_final: 0.8261 (t0) REVERT: A 988 GLU cc_start: 0.9053 (mp0) cc_final: 0.8590 (pm20) REVERT: B 55 PHE cc_start: 0.8125 (m-80) cc_final: 0.7447 (m-80) REVERT: B 177 MET cc_start: 0.7113 (pmm) cc_final: 0.6452 (pmm) REVERT: B 223 LEU cc_start: 0.8128 (mp) cc_final: 0.7874 (mt) REVERT: B 224 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: B 242 LEU cc_start: 0.8123 (mm) cc_final: 0.7593 (mp) REVERT: B 269 TYR cc_start: 0.7723 (m-80) cc_final: 0.7427 (m-10) REVERT: B 330 PRO cc_start: 0.8537 (Cg_exo) cc_final: 0.8237 (Cg_endo) REVERT: B 571 ASP cc_start: 0.8509 (m-30) cc_final: 0.8204 (t0) REVERT: B 725 GLU cc_start: 0.8922 (tt0) cc_final: 0.8682 (tt0) REVERT: B 768 THR cc_start: 0.9210 (m) cc_final: 0.8981 (p) REVERT: B 955 ASN cc_start: 0.8673 (m110) cc_final: 0.8395 (t0) REVERT: C 52 GLN cc_start: 0.8579 (tm-30) cc_final: 0.7973 (tp40) REVERT: C 220 PHE cc_start: 0.6578 (t80) cc_final: 0.6233 (t80) REVERT: C 324 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: C 351 TYR cc_start: 0.8906 (p90) cc_final: 0.8519 (p90) REVERT: C 434 ILE cc_start: 0.4603 (OUTLIER) cc_final: 0.4296 (mt) REVERT: C 497 PHE cc_start: 0.3103 (m-10) cc_final: 0.2756 (m-80) REVERT: C 756 TYR cc_start: 0.8994 (m-80) cc_final: 0.8742 (m-80) REVERT: C 765 ARG cc_start: 0.8738 (mtt90) cc_final: 0.8448 (mtm-85) REVERT: C 773 GLU cc_start: 0.8674 (tt0) cc_final: 0.8300 (tt0) REVERT: C 856 ASN cc_start: 0.9248 (OUTLIER) cc_final: 0.8981 (m110) REVERT: C 900 MET cc_start: 0.9158 (mtm) cc_final: 0.8923 (mtm) REVERT: C 923 ILE cc_start: 0.9612 (OUTLIER) cc_final: 0.9372 (mp) REVERT: C 950 ASP cc_start: 0.8799 (m-30) cc_final: 0.8361 (m-30) REVERT: C 984 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7693 (tp) REVERT: C 987 PRO cc_start: 0.8153 (Cg_exo) cc_final: 0.7720 (Cg_endo) REVERT: C 1017 GLU cc_start: 0.9100 (tt0) cc_final: 0.8850 (tt0) outliers start: 52 outliers final: 37 residues processed: 241 average time/residue: 0.3095 time to fit residues: 123.0616 Evaluate side-chains 232 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 185 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 252 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C 960 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.105062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.067803 restraints weight = 53563.656| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.29 r_work: 0.2964 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.7210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 22844 Z= 0.168 Angle : 0.575 12.318 31183 Z= 0.290 Chirality : 0.044 0.209 3703 Planarity : 0.004 0.071 3920 Dihedral : 4.923 56.521 4085 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.23 % Allowed : 16.05 % Favored : 81.71 % 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: 0.90 (0.16), residues: 2699 helix: 2.44 (0.20), residues: 665 sheet: 0.26 (0.19), residues: 642 loop : -0.09 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 104 HIS 0.006 0.001 HIS C1048 PHE 0.024 0.001 PHE B 823 TYR 0.030 0.001 TYR B 170 ARG 0.005 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 37) link_NAG-ASN : angle 1.68277 ( 111) link_BETA1-4 : bond 0.00229 ( 18) link_BETA1-4 : angle 1.07824 ( 54) hydrogen bonds : bond 0.03676 ( 985) hydrogen bonds : angle 5.09677 ( 2868) SS BOND : bond 0.00194 ( 34) SS BOND : angle 1.04213 ( 68) covalent geometry : bond 0.00385 (22755) covalent geometry : angle 0.56467 (30950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8609 (mm) cc_final: 0.8245 (tp) REVERT: A 52 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8510 (tm-30) REVERT: A 99 ASN cc_start: 0.8355 (m-40) cc_final: 0.7657 (p0) REVERT: A 101 ILE cc_start: 0.8360 (mp) cc_final: 0.8054 (mm) REVERT: A 173 GLN cc_start: 0.8608 (pm20) cc_final: 0.8330 (tp40) REVERT: A 200 TYR cc_start: 0.8092 (m-80) cc_final: 0.7696 (m-80) REVERT: A 201 PHE cc_start: 0.8502 (t80) cc_final: 0.8251 (t80) REVERT: A 314 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8446 (tm-30) REVERT: A 759 PHE cc_start: 0.8655 (m-80) cc_final: 0.8280 (m-80) REVERT: A 955 ASN cc_start: 0.8653 (m-40) cc_final: 0.8423 (t0) REVERT: A 988 GLU cc_start: 0.9061 (mp0) cc_final: 0.8623 (pm20) REVERT: B 55 PHE cc_start: 0.8114 (m-80) cc_final: 0.7533 (m-80) REVERT: B 177 MET cc_start: 0.7234 (pmm) cc_final: 0.7019 (pmm) REVERT: B 223 LEU cc_start: 0.8158 (mp) cc_final: 0.7925 (mt) REVERT: B 224 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: B 269 TYR cc_start: 0.7834 (m-80) cc_final: 0.7611 (m-10) REVERT: B 571 ASP cc_start: 0.8479 (m-30) cc_final: 0.8186 (t0) REVERT: B 725 GLU cc_start: 0.8887 (tt0) cc_final: 0.8672 (tt0) REVERT: B 738 CYS cc_start: 0.8095 (t) cc_final: 0.7834 (t) REVERT: B 955 ASN cc_start: 0.8701 (m110) cc_final: 0.8439 (t0) REVERT: C 52 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8488 (tm-30) REVERT: C 177 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6630 (ptt) REVERT: C 220 PHE cc_start: 0.6828 (t80) cc_final: 0.6513 (t80) REVERT: C 324 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8009 (pm20) REVERT: C 351 TYR cc_start: 0.8863 (p90) cc_final: 0.8529 (p90) REVERT: C 434 ILE cc_start: 0.4774 (OUTLIER) cc_final: 0.4471 (mt) REVERT: C 765 ARG cc_start: 0.8809 (mtt90) cc_final: 0.8508 (mtm-85) REVERT: C 773 GLU cc_start: 0.8699 (tt0) cc_final: 0.8379 (tt0) REVERT: C 900 MET cc_start: 0.9198 (mtm) cc_final: 0.8941 (mtm) REVERT: C 923 ILE cc_start: 0.9668 (OUTLIER) cc_final: 0.9438 (mp) REVERT: C 950 ASP cc_start: 0.8791 (m-30) cc_final: 0.8297 (m-30) REVERT: C 984 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7601 (tp) REVERT: C 988 GLU cc_start: 0.8784 (mp0) cc_final: 0.8506 (tp30) REVERT: C 1017 GLU cc_start: 0.9063 (tt0) cc_final: 0.8862 (tt0) outliers start: 54 outliers final: 41 residues processed: 233 average time/residue: 0.3022 time to fit residues: 116.6754 Evaluate side-chains 231 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 147 optimal weight: 2.9990 chunk 84 optimal weight: 0.0770 chunk 104 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 205 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 228 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.105070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.067873 restraints weight = 53148.973| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.24 r_work: 0.2968 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.7218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.261 22844 Z= 0.201 Angle : 0.732 59.200 31183 Z= 0.406 Chirality : 0.046 0.745 3703 Planarity : 0.004 0.070 3920 Dihedral : 4.945 56.549 4085 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.07 % Allowed : 16.30 % Favored : 81.63 % Cbeta Deviations : 0.04 % 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: 0.89 (0.16), residues: 2699 helix: 2.42 (0.20), residues: 665 sheet: 0.26 (0.19), residues: 642 loop : -0.09 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 104 HIS 0.004 0.001 HIS C1048 PHE 0.026 0.001 PHE C1052 TYR 0.061 0.001 TYR C 451 ARG 0.029 0.001 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 37) link_NAG-ASN : angle 1.68460 ( 111) link_BETA1-4 : bond 0.00220 ( 18) link_BETA1-4 : angle 1.09100 ( 54) hydrogen bonds : bond 0.03670 ( 985) hydrogen bonds : angle 5.11545 ( 2868) SS BOND : bond 0.00243 ( 34) SS BOND : angle 1.06788 ( 68) covalent geometry : bond 0.00482 (22755) covalent geometry : angle 0.72448 (30950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12763.29 seconds wall clock time: 219 minutes 5.69 seconds (13145.69 seconds total)