Starting phenix.real_space_refine on Fri Sep 19 03:04:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm1_27523/09_2025/8dm1_27523.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm1_27523/09_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_27523/09_2025/8dm1_27523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm1_27523/09_2025/8dm1_27523.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm1_27523/09_2025/8dm1_27523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm1_27523/09_2025/8dm1_27523.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.62, per 1000 atoms: 0.21 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: 1.84 Conformation dependent library (CDL) restraints added in 916.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.96 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: 5.30 Time building geometry restraints manager: 2.43 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 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: 5.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.200 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.170 ------------------------------------------------------------------------------- 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 : 3.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.016 0.001 ARG A 273 TYR 0.032 0.002 TYR C1067 PHE 0.027 0.002 PHE C 371 TRP 0.022 0.002 TRP A 64 HIS 0.018 0.002 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00530 (22755) covalent geometry : angle 0.83752 (30950) SS BOND : bond 0.00309 ( 34) SS BOND : angle 1.46389 ( 68) hydrogen bonds : bond 0.11714 ( 985) hydrogen bonds : angle 7.20150 ( 2868) link_BETA1-4 : bond 0.00650 ( 18) link_BETA1-4 : angle 1.54008 ( 54) link_NAG-ASN : bond 0.00341 ( 37) link_NAG-ASN : angle 2.51792 ( 111) *********************** 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 : 0.854 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 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: 0.7571 (t) REVERT: A 858 LEU cc_start: 0.8335 (mt) cc_final: 0.8115 (mt) REVERT: B 42 VAL cc_start: 0.7924 (t) cc_final: 0.7352 (t) REVERT: B 55 PHE cc_start: 0.8208 (m-80) cc_final: 0.7670 (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: 0.6197 (mp) REVERT: B 226 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7841 (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: 0.7456 (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: 0.7523 (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: 0.6939 (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: 0.9176 (tt) REVERT: C 191 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7068 (mt-10) 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: 0.6278 (m-80) REVERT: C 574 ASP cc_start: 0.7487 (t0) cc_final: 0.7224 (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: 0.1475 time to fit residues: 130.5430 Evaluate side-chains 301 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 296 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 606 ASN A 613 GLN A 710 ASN A 957 GLN A1142 GLN B 115 GLN B 245 HIS B 641 ASN B 901 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 HIS ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 926 GLN C 954 HIS C1002 GLN C1010 GLN C1011 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.108766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.071525 restraints weight = 53490.324| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.32 r_work: 0.3030 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 22844 Z= 0.248 Angle : 0.806 24.356 31183 Z= 0.403 Chirality : 0.055 1.239 3703 Planarity : 0.006 0.095 3920 Dihedral : 7.166 59.757 4096 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.19 % Allowed : 11.13 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.15), residues: 2699 helix: 1.34 (0.19), residues: 667 sheet: 0.26 (0.19), residues: 603 loop : -0.44 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C1107 TYR 0.039 0.002 TYR A 660 PHE 0.037 0.003 PHE B 220 TRP 0.026 0.002 TRP A 104 HIS 0.008 0.002 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00549 (22755) covalent geometry : angle 0.78479 (30950) SS BOND : bond 0.00356 ( 34) SS BOND : angle 1.44382 ( 68) hydrogen bonds : bond 0.04803 ( 985) hydrogen bonds : angle 5.86175 ( 2868) link_BETA1-4 : bond 0.00351 ( 18) link_BETA1-4 : angle 1.59775 ( 54) link_NAG-ASN : bond 0.00758 ( 37) link_NAG-ASN : angle 2.84626 ( 111) *********************** 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 366 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 289 time to evaluate : 0.594 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: 0.7685 (m-90) cc_final: 0.7373 (m-90) REVERT: A 137 ASN cc_start: 0.7554 (m110) cc_final: 0.6827 (p0) REVERT: A 200 TYR cc_start: 0.8098 (m-80) cc_final: 0.7795 (m-80) REVERT: A 201 PHE cc_start: 0.8095 (t80) cc_final: 0.7720 (t80) REVERT: A 314 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8435 (tm-30) REVERT: A 953 ASN cc_start: 0.8844 (m-40) cc_final: 0.8595 (m-40) REVERT: A 955 ASN cc_start: 0.8605 (m-40) cc_final: 0.8283 (t0) REVERT: B 55 PHE cc_start: 0.8344 (m-80) cc_final: 0.7574 (m-80) REVERT: B 177 MET cc_start: 0.7523 (pmm) cc_final: 0.7193 (pmm) REVERT: B 200 TYR cc_start: 0.8022 (m-80) cc_final: 0.7717 (m-80) REVERT: B 305 SER cc_start: 0.9062 (t) cc_final: 0.8820 (p) REVERT: B 751 ASN cc_start: 0.9059 (m-40) cc_final: 0.8853 (m110) REVERT: B 970 PHE cc_start: 0.8919 (m-80) cc_final: 0.8587 (m-80) REVERT: B 979 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8351 (t0) REVERT: C 52 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7400 (tp40) REVERT: C 53 ASP cc_start: 0.7760 (t0) cc_final: 0.7426 (t0) REVERT: C 235 ILE cc_start: 0.6383 (mt) cc_final: 0.6151 (mt) REVERT: C 238 PHE cc_start: 0.6819 (p90) cc_final: 0.6353 (p90) REVERT: C 351 TYR cc_start: 0.8731 (p90) cc_final: 0.8263 (p90) REVERT: C 380 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7765 (m-10) REVERT: C 574 ASP cc_start: 0.7915 (t0) cc_final: 0.7685 (t0) REVERT: C 950 ASP cc_start: 0.8689 (m-30) cc_final: 0.8303 (m-30) REVERT: C 957 GLN cc_start: 0.8678 (tt0) cc_final: 0.8466 (tt0) REVERT: C 984 LEU cc_start: 0.7399 (tp) cc_final: 0.7111 (tt) REVERT: C 994 ASP cc_start: 0.8783 (m-30) cc_final: 0.8336 (m-30) REVERT: C 1142 GLN cc_start: 0.8683 (tp40) cc_final: 0.8431 (tm-30) outliers start: 77 outliers final: 42 residues processed: 345 average time/residue: 0.1369 time to fit residues: 75.7698 Evaluate side-chains 264 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 220 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 907 ASN 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 985 ASP 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 289 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 380 TYR 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 696 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 915 VAL 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 1018 ILE Chi-restraints excluded: chain C residue 1051 SER 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 226 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 271 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 264 optimal weight: 0.0270 chunk 69 optimal weight: 0.9980 chunk 230 optimal weight: 0.8980 chunk 148 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 314 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 957 GLN B1002 GLN B1011 GLN B1058 HIS C 965 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.108617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.071557 restraints weight = 53118.520| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.30 r_work: 0.3029 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22844 Z= 0.132 Angle : 0.566 9.192 31183 Z= 0.289 Chirality : 0.044 0.176 3703 Planarity : 0.004 0.054 3920 Dihedral : 6.200 58.763 4089 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.32 % Allowed : 13.24 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.16), residues: 2699 helix: 2.05 (0.19), residues: 666 sheet: 0.31 (0.19), residues: 633 loop : -0.28 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.022 0.001 TYR A1067 PHE 0.027 0.001 PHE C 855 TRP 0.012 0.001 TRP C 436 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00292 (22755) covalent geometry : angle 0.55095 (30950) SS BOND : bond 0.00181 ( 34) SS BOND : angle 1.16404 ( 68) hydrogen bonds : bond 0.03962 ( 985) hydrogen bonds : angle 5.46145 ( 2868) link_BETA1-4 : bond 0.00407 ( 18) link_BETA1-4 : angle 1.19407 ( 54) link_NAG-ASN : bond 0.00324 ( 37) link_NAG-ASN : angle 1.94479 ( 111) *********************** 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 291 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 235 time to evaluate : 0.775 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 104 TRP cc_start: 0.7759 (m-90) cc_final: 0.7529 (m-90) REVERT: A 201 PHE cc_start: 0.8191 (t80) cc_final: 0.7643 (t80) REVERT: A 314 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8305 (tm-30) REVERT: A 955 ASN cc_start: 0.8584 (m-40) cc_final: 0.8339 (t0) REVERT: B 55 PHE cc_start: 0.8156 (m-80) cc_final: 0.7504 (m-80) REVERT: B 177 MET cc_start: 0.7257 (pmm) cc_final: 0.6895 (pmm) REVERT: B 242 LEU cc_start: 0.7937 (mm) cc_final: 0.7593 (mm) REVERT: B 305 SER cc_start: 0.9086 (t) cc_final: 0.8855 (p) REVERT: B 309 GLU cc_start: 0.8966 (mp0) cc_final: 0.8744 (mp0) REVERT: B 330 PRO cc_start: 0.8598 (Cg_exo) cc_final: 0.8303 (Cg_endo) REVERT: B 955 ASN cc_start: 0.8244 (m110) cc_final: 0.7848 (t0) REVERT: B 970 PHE cc_start: 0.8921 (m-80) cc_final: 0.8667 (m-80) REVERT: B 979 ASP cc_start: 0.8528 (t0) cc_final: 0.8303 (t0) REVERT: C 52 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7510 (tp40) REVERT: C 99 ASN cc_start: 0.8136 (p0) cc_final: 0.6974 (t0) REVERT: C 191 GLU cc_start: 0.8563 (mt-10) cc_final: 0.7716 (mp0) REVERT: C 235 ILE cc_start: 0.6468 (mt) cc_final: 0.6254 (mt) REVERT: C 238 PHE cc_start: 0.6751 (p90) cc_final: 0.6278 (p90) REVERT: C 351 TYR cc_start: 0.8803 (p90) cc_final: 0.8225 (p90) REVERT: C 855 PHE cc_start: 0.8424 (m-80) cc_final: 0.7871 (m-80) REVERT: C 933 LYS cc_start: 0.8431 (mmtm) cc_final: 0.8069 (mttm) REVERT: C 950 ASP cc_start: 0.8772 (m-30) cc_final: 0.8289 (m-30) REVERT: C 957 GLN cc_start: 0.8703 (tt0) cc_final: 0.8485 (tt0) REVERT: C 1142 GLN cc_start: 0.8657 (tp40) cc_final: 0.8250 (tp40) outliers start: 56 outliers final: 41 residues processed: 275 average time/residue: 0.1377 time to fit residues: 61.8089 Evaluate side-chains 254 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 900 MET 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 42 VAL 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 1010 GLN Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 189 LEU 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 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 991 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 84 optimal weight: 0.7980 chunk 233 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 171 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 172 optimal weight: 0.1980 chunk 211 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 23 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN C 824 ASN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.107959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.070794 restraints weight = 53084.438| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.31 r_work: 0.3013 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.5201 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= 0.138 Angle : 0.548 8.249 31183 Z= 0.281 Chirality : 0.044 0.176 3703 Planarity : 0.004 0.049 3920 Dihedral : 5.683 58.198 4089 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.69 % Allowed : 13.53 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.16), residues: 2699 helix: 2.16 (0.20), residues: 667 sheet: 0.29 (0.19), residues: 641 loop : -0.20 (0.16), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 273 TYR 0.021 0.001 TYR A1067 PHE 0.028 0.001 PHE C 392 TRP 0.014 0.001 TRP B 104 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00304 (22755) covalent geometry : angle 0.53422 (30950) SS BOND : bond 0.00143 ( 34) SS BOND : angle 1.05451 ( 68) hydrogen bonds : bond 0.03739 ( 985) hydrogen bonds : angle 5.21671 ( 2868) link_BETA1-4 : bond 0.00249 ( 18) link_BETA1-4 : angle 1.16192 ( 54) link_NAG-ASN : bond 0.00309 ( 37) link_NAG-ASN : angle 1.84975 ( 111) *********************** 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 301 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 236 time to evaluate : 0.842 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: 0.8518 (mm) cc_final: 0.8098 (tp) REVERT: A 200 TYR cc_start: 0.8107 (m-80) cc_final: 0.7806 (m-80) REVERT: A 214 ARG cc_start: 0.7116 (tpt-90) cc_final: 0.6907 (tpt-90) REVERT: A 314 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8298 (tm-30) REVERT: A 955 ASN cc_start: 0.8608 (m-40) cc_final: 0.8317 (t0) REVERT: B 55 PHE cc_start: 0.8065 (m-80) cc_final: 0.7424 (m-80) REVERT: B 177 MET cc_start: 0.7213 (pmm) cc_final: 0.6642 (pmm) REVERT: B 242 LEU cc_start: 0.8017 (mm) cc_final: 0.7615 (mm) REVERT: B 309 GLU cc_start: 0.9007 (mp0) cc_final: 0.8807 (mp0) REVERT: B 330 PRO cc_start: 0.8610 (Cg_exo) cc_final: 0.8323 (Cg_endo) REVERT: B 979 ASP cc_start: 0.8501 (t0) cc_final: 0.8216 (t0) REVERT: C 52 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7610 (tp40) REVERT: C 53 ASP cc_start: 0.7559 (t0) cc_final: 0.7338 (t70) REVERT: C 99 ASN cc_start: 0.8193 (p0) cc_final: 0.7243 (t0) REVERT: C 238 PHE cc_start: 0.6846 (p90) cc_final: 0.6354 (p90) REVERT: C 314 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7703 (tp-100) REVERT: C 351 TYR cc_start: 0.8804 (p90) cc_final: 0.8273 (p90) REVERT: C 574 ASP cc_start: 0.8109 (t0) cc_final: 0.7893 (t0) REVERT: C 855 PHE cc_start: 0.8514 (m-80) cc_final: 0.8100 (m-80) REVERT: C 856 ASN cc_start: 0.9306 (m110) cc_final: 0.8987 (m-40) REVERT: C 923 ILE cc_start: 0.9574 (OUTLIER) cc_final: 0.9357 (mp) REVERT: C 933 LYS cc_start: 0.8510 (mmtm) cc_final: 0.8214 (mttm) REVERT: C 950 ASP cc_start: 0.8785 (m-30) cc_final: 0.8287 (m-30) REVERT: C 957 GLN cc_start: 0.8784 (tt0) cc_final: 0.8545 (tt0) REVERT: C 1145 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7081 (pp) outliers start: 65 outliers final: 43 residues processed: 280 average time/residue: 0.1332 time to fit residues: 61.2537 Evaluate side-chains 252 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 226 LEU 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 565 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 752 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 959 LEU 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 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 42 VAL 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 747 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 968 SER 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 430 THR Chi-restraints excluded: chain C residue 489 TYR 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 791 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 126 optimal weight: 0.9980 chunk 267 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 824 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 30 ASN C 245 HIS C 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.106624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.069203 restraints weight = 52594.625| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.44 r_work: 0.2946 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22844 Z= 0.169 Angle : 0.561 8.607 31183 Z= 0.286 Chirality : 0.045 0.170 3703 Planarity : 0.004 0.050 3920 Dihedral : 5.448 58.558 4089 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.44 % Allowed : 14.65 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.16), residues: 2699 helix: 2.19 (0.19), residues: 666 sheet: 0.22 (0.18), residues: 653 loop : -0.20 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 403 TYR 0.021 0.001 TYR A1067 PHE 0.030 0.001 PHE B 220 TRP 0.017 0.001 TRP B 104 HIS 0.019 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00382 (22755) covalent geometry : angle 0.54889 (30950) SS BOND : bond 0.00197 ( 34) SS BOND : angle 1.05944 ( 68) hydrogen bonds : bond 0.03809 ( 985) hydrogen bonds : angle 5.20954 ( 2868) link_BETA1-4 : bond 0.00237 ( 18) link_BETA1-4 : angle 1.15308 ( 54) link_NAG-ASN : bond 0.00310 ( 37) link_NAG-ASN : angle 1.78262 ( 111) *********************** 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 285 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 226 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8590 (mm) cc_final: 0.8077 (tp) REVERT: A 200 TYR cc_start: 0.8091 (m-80) cc_final: 0.6939 (m-80) REVERT: A 748 GLU cc_start: 0.9045 (mp0) cc_final: 0.8791 (mp0) REVERT: A 786 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8409 (mmmt) REVERT: A 955 ASN cc_start: 0.8665 (m-40) cc_final: 0.8137 (t0) REVERT: A 995 ARG cc_start: 0.9010 (mtp-110) cc_final: 0.8223 (mtp85) REVERT: B 55 PHE cc_start: 0.8082 (m-80) cc_final: 0.7404 (m-80) REVERT: B 177 MET cc_start: 0.7397 (pmm) cc_final: 0.6743 (pmm) REVERT: B 242 LEU cc_start: 0.7946 (mm) cc_final: 0.7604 (mm) REVERT: B 309 GLU cc_start: 0.9056 (mp0) cc_final: 0.8630 (mp0) REVERT: B 313 TYR cc_start: 0.8825 (m-80) cc_final: 0.8355 (m-80) REVERT: B 330 PRO cc_start: 0.8697 (Cg_exo) cc_final: 0.8435 (Cg_endo) REVERT: B 725 GLU cc_start: 0.8825 (tt0) cc_final: 0.8509 (tt0) REVERT: B 764 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8370 (ttpp) REVERT: B 955 ASN cc_start: 0.8449 (m110) cc_final: 0.8034 (t0) REVERT: B 979 ASP cc_start: 0.8299 (t0) cc_final: 0.8033 (t0) REVERT: B 988 GLU cc_start: 0.9061 (tp30) cc_final: 0.8774 (tp30) REVERT: C 50 SER cc_start: 0.9542 (p) cc_final: 0.9224 (m) REVERT: C 52 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7722 (tp40) REVERT: C 238 PHE cc_start: 0.6881 (p90) cc_final: 0.6504 (p90) REVERT: C 324 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: C 351 TYR cc_start: 0.8861 (p90) cc_final: 0.8476 (p90) REVERT: C 572 THR cc_start: 0.7651 (m) cc_final: 0.7379 (p) REVERT: C 574 ASP cc_start: 0.8009 (t0) cc_final: 0.7706 (t0) REVERT: C 758 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8324 (p) REVERT: C 762 GLN cc_start: 0.9228 (mt0) cc_final: 0.9009 (mt0) REVERT: C 773 GLU cc_start: 0.8581 (tt0) cc_final: 0.8057 (tt0) REVERT: C 855 PHE cc_start: 0.8593 (m-80) cc_final: 0.8195 (m-80) REVERT: C 856 ASN cc_start: 0.9282 (m110) cc_final: 0.8919 (m-40) REVERT: C 923 ILE cc_start: 0.9463 (OUTLIER) cc_final: 0.9194 (mp) REVERT: C 933 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8204 (mttm) REVERT: C 950 ASP cc_start: 0.8767 (m-30) cc_final: 0.8297 (m-30) REVERT: C 957 GLN cc_start: 0.8790 (tt0) cc_final: 0.8588 (tt0) REVERT: C 1092 GLU cc_start: 0.8546 (pm20) cc_final: 0.8229 (pm20) outliers start: 59 outliers final: 41 residues processed: 268 average time/residue: 0.1432 time to fit residues: 62.5526 Evaluate side-chains 241 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR 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 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 131 CYS 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 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 1010 GLN 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 375 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR 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 697 MET Chi-restraints excluded: chain C residue 758 SER 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 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 99 optimal weight: 20.0000 chunk 272 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.104963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.067298 restraints weight = 53052.628| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.46 r_work: 0.2898 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.6586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 22844 Z= 0.211 Angle : 0.595 12.684 31183 Z= 0.302 Chirality : 0.045 0.188 3703 Planarity : 0.004 0.076 3920 Dihedral : 5.316 54.539 4087 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.10 % Allowed : 14.56 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.16), residues: 2699 helix: 2.10 (0.19), residues: 666 sheet: 0.06 (0.18), residues: 662 loop : -0.18 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 357 TYR 0.029 0.002 TYR B 170 PHE 0.025 0.002 PHE B 823 TRP 0.018 0.002 TRP B 258 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00480 (22755) covalent geometry : angle 0.58195 (30950) SS BOND : bond 0.00204 ( 34) SS BOND : angle 1.09809 ( 68) hydrogen bonds : bond 0.03974 ( 985) hydrogen bonds : angle 5.28613 ( 2868) link_BETA1-4 : bond 0.00193 ( 18) link_BETA1-4 : angle 1.16306 ( 54) link_NAG-ASN : bond 0.00391 ( 37) link_NAG-ASN : angle 1.86162 ( 111) *********************** 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 276 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 201 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8666 (mm) cc_final: 0.8147 (tp) REVERT: A 157 PHE cc_start: 0.7855 (m-10) cc_final: 0.7651 (m-10) REVERT: A 200 TYR cc_start: 0.8121 (m-80) cc_final: 0.7544 (m-80) REVERT: A 314 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8242 (tm-30) REVERT: A 748 GLU cc_start: 0.9105 (mp0) cc_final: 0.8854 (mp0) REVERT: A 955 ASN cc_start: 0.8663 (m-40) cc_final: 0.8135 (t0) REVERT: A 988 GLU cc_start: 0.9064 (mp0) cc_final: 0.8664 (pm20) REVERT: A 995 ARG cc_start: 0.9074 (mtp-110) cc_final: 0.8228 (mtp85) REVERT: B 55 PHE cc_start: 0.8050 (m-80) cc_final: 0.7451 (m-80) REVERT: B 177 MET cc_start: 0.7354 (pmm) cc_final: 0.7014 (pmm) REVERT: B 242 LEU cc_start: 0.8044 (mm) cc_final: 0.7709 (mm) REVERT: B 571 ASP cc_start: 0.8536 (m-30) cc_final: 0.8334 (t0) REVERT: B 725 GLU cc_start: 0.8904 (tt0) cc_final: 0.8614 (tt0) REVERT: B 745 ASP cc_start: 0.8571 (p0) cc_final: 0.8211 (p0) REVERT: B 955 ASN cc_start: 0.8622 (m110) cc_final: 0.8115 (t0) REVERT: B 988 GLU cc_start: 0.9186 (tp30) cc_final: 0.8857 (tp30) REVERT: C 52 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7629 (tp40) REVERT: C 53 ASP cc_start: 0.7732 (t0) cc_final: 0.7278 (t0) REVERT: C 309 GLU cc_start: 0.8808 (mp0) cc_final: 0.8505 (mp0) REVERT: C 324 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7804 (pm20) REVERT: C 351 TYR cc_start: 0.8881 (p90) cc_final: 0.8548 (p90) REVERT: C 512 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7529 (p) REVERT: C 572 THR cc_start: 0.7699 (m) cc_final: 0.7349 (p) REVERT: C 574 ASP cc_start: 0.8058 (t0) cc_final: 0.7749 (t0) REVERT: C 773 GLU cc_start: 0.8620 (tt0) cc_final: 0.8145 (tt0) REVERT: C 855 PHE cc_start: 0.8574 (m-80) cc_final: 0.8194 (m-80) REVERT: C 923 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9207 (mp) REVERT: C 957 GLN cc_start: 0.8822 (tt0) cc_final: 0.8615 (tt0) REVERT: C 1092 GLU cc_start: 0.8578 (pm20) cc_final: 0.8292 (pm20) outliers start: 75 outliers final: 52 residues processed: 257 average time/residue: 0.1324 time to fit residues: 56.1966 Evaluate side-chains 241 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 186 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 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 303 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU 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 963 VAL Chi-restraints excluded: chain A residue 966 LEU 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 18 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 131 CYS 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 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 724 THR 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 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 208 THR 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 375 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE 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 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1017 GLU 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 100 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 210 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B 978 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 450 ASN C 960 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.102459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.064974 restraints weight = 53470.297| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.43 r_work: 0.2846 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.7310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 22844 Z= 0.311 Angle : 0.672 9.900 31183 Z= 0.341 Chirality : 0.047 0.197 3703 Planarity : 0.004 0.048 3920 Dihedral : 5.599 54.214 4087 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.61 % Allowed : 15.35 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.16), residues: 2699 helix: 1.96 (0.19), residues: 667 sheet: -0.14 (0.19), residues: 638 loop : -0.33 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 357 TYR 0.022 0.002 TYR A1067 PHE 0.024 0.002 PHE C 392 TRP 0.025 0.002 TRP B 258 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00711 (22755) covalent geometry : angle 0.65865 (30950) SS BOND : bond 0.00303 ( 34) SS BOND : angle 1.23559 ( 68) hydrogen bonds : bond 0.04319 ( 985) hydrogen bonds : angle 5.51031 ( 2868) link_BETA1-4 : bond 0.00203 ( 18) link_BETA1-4 : angle 1.21633 ( 54) link_NAG-ASN : bond 0.00555 ( 37) link_NAG-ASN : angle 2.06846 ( 111) *********************** 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 260 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 197 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8804 (mm) cc_final: 0.8304 (tp) REVERT: A 52 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8358 (tm-30) REVERT: A 104 TRP cc_start: 0.7609 (m-90) cc_final: 0.7345 (m-90) REVERT: A 200 TYR cc_start: 0.8050 (m-80) cc_final: 0.7586 (m-80) REVERT: A 214 ARG cc_start: 0.7203 (tpt-90) cc_final: 0.6958 (tpt-90) REVERT: A 314 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8255 (tm-30) REVERT: A 615 VAL cc_start: 0.9440 (OUTLIER) cc_final: 0.9179 (m) REVERT: A 748 GLU cc_start: 0.9153 (mp0) cc_final: 0.8881 (mp0) REVERT: A 955 ASN cc_start: 0.8658 (m-40) cc_final: 0.8301 (t0) REVERT: A 988 GLU cc_start: 0.9072 (mp0) cc_final: 0.8701 (pm20) REVERT: B 55 PHE cc_start: 0.8169 (m-80) cc_final: 0.7683 (m-80) REVERT: B 66 HIS cc_start: 0.5400 (OUTLIER) cc_final: 0.5172 (t70) REVERT: B 170 TYR cc_start: 0.7891 (t80) cc_final: 0.7543 (t80) REVERT: B 177 MET cc_start: 0.7293 (pmm) cc_final: 0.6948 (pmm) REVERT: B 242 LEU cc_start: 0.8046 (mm) cc_final: 0.7729 (mm) REVERT: B 571 ASP cc_start: 0.8621 (m-30) cc_final: 0.8369 (t0) REVERT: B 725 GLU cc_start: 0.8917 (tt0) cc_final: 0.8631 (tt0) REVERT: B 853 GLN cc_start: 0.7776 (mt0) cc_final: 0.7476 (mt0) REVERT: B 955 ASN cc_start: 0.8679 (m110) cc_final: 0.8281 (t0) REVERT: B 988 GLU cc_start: 0.9229 (tp30) cc_final: 0.8816 (tp30) REVERT: C 52 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8294 (tm-30) REVERT: C 324 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7833 (pm20) REVERT: C 351 TYR cc_start: 0.8924 (p90) cc_final: 0.8722 (p90) REVERT: C 512 VAL cc_start: 0.8121 (OUTLIER) cc_final: 0.7673 (p) REVERT: C 572 THR cc_start: 0.7707 (m) cc_final: 0.7481 (p) REVERT: C 574 ASP cc_start: 0.8106 (t0) cc_final: 0.7812 (t0) REVERT: C 773 GLU cc_start: 0.8652 (tt0) cc_final: 0.8232 (tt0) REVERT: C 855 PHE cc_start: 0.8574 (m-10) cc_final: 0.8170 (m-80) REVERT: C 923 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9188 (mp) REVERT: C 957 GLN cc_start: 0.8832 (tt0) cc_final: 0.8632 (tt0) REVERT: C 988 GLU cc_start: 0.9009 (mp0) cc_final: 0.8532 (tp30) REVERT: C 994 ASP cc_start: 0.8598 (m-30) cc_final: 0.8366 (t70) REVERT: C 1092 GLU cc_start: 0.8564 (pm20) cc_final: 0.8285 (pm20) outliers start: 63 outliers final: 48 residues processed: 250 average time/residue: 0.1439 time to fit residues: 58.3629 Evaluate side-chains 232 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 179 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 303 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU 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 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU 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 997 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 131 CYS 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 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 957 GLN 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 131 CYS 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 375 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU 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 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1018 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 50 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 146 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 172 optimal weight: 4.9990 chunk 250 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 91 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 755 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN 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 = 0.3815 r_free = 0.3815 target = 0.105109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067857 restraints weight = 52642.892| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.46 r_work: 0.2914 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.7367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22844 Z= 0.123 Angle : 0.571 11.964 31183 Z= 0.291 Chirality : 0.044 0.207 3703 Planarity : 0.004 0.046 3920 Dihedral : 5.304 55.031 4085 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.99 % Allowed : 16.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.16), residues: 2699 helix: 2.22 (0.19), residues: 660 sheet: -0.03 (0.18), residues: 652 loop : -0.23 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.021 0.001 TYR A1067 PHE 0.033 0.001 PHE B 168 TRP 0.025 0.002 TRP A 104 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00272 (22755) covalent geometry : angle 0.56050 (30950) SS BOND : bond 0.00182 ( 34) SS BOND : angle 1.05699 ( 68) hydrogen bonds : bond 0.03729 ( 985) hydrogen bonds : angle 5.22933 ( 2868) link_BETA1-4 : bond 0.00334 ( 18) link_BETA1-4 : angle 0.96548 ( 54) link_NAG-ASN : bond 0.00253 ( 37) link_NAG-ASN : angle 1.70686 ( 111) *********************** 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 254 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8781 (mm) cc_final: 0.8350 (tp) REVERT: A 52 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8384 (tm-30) REVERT: A 200 TYR cc_start: 0.7928 (m-80) cc_final: 0.7471 (m-80) REVERT: A 748 GLU cc_start: 0.9171 (mp0) cc_final: 0.8921 (mp0) REVERT: A 754 LEU cc_start: 0.9336 (mp) cc_final: 0.9136 (mp) REVERT: A 955 ASN cc_start: 0.8663 (m-40) cc_final: 0.8212 (t0) REVERT: A 988 GLU cc_start: 0.9035 (mp0) cc_final: 0.8638 (pm20) REVERT: A 995 ARG cc_start: 0.9136 (mtp-110) cc_final: 0.8452 (mtp85) REVERT: B 55 PHE cc_start: 0.8118 (m-80) cc_final: 0.7571 (m-80) REVERT: B 170 TYR cc_start: 0.7909 (t80) cc_final: 0.7547 (t80) REVERT: B 177 MET cc_start: 0.7136 (pmm) cc_final: 0.6807 (pmm) REVERT: B 242 LEU cc_start: 0.8154 (mm) cc_final: 0.7622 (mp) REVERT: B 571 ASP cc_start: 0.8593 (m-30) cc_final: 0.8352 (t0) REVERT: B 725 GLU cc_start: 0.8883 (tt0) cc_final: 0.8526 (tt0) REVERT: B 755 GLN cc_start: 0.9174 (mt0) cc_final: 0.8850 (tt0) REVERT: B 988 GLU cc_start: 0.9214 (tp30) cc_final: 0.8808 (tp30) REVERT: C 52 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8250 (tm-30) REVERT: C 324 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7898 (pm20) REVERT: C 351 TYR cc_start: 0.8923 (p90) cc_final: 0.8696 (p90) REVERT: C 497 PHE cc_start: 0.3071 (m-80) cc_final: 0.2822 (m-80) REVERT: C 572 THR cc_start: 0.7610 (m) cc_final: 0.7339 (p) REVERT: C 773 GLU cc_start: 0.8597 (tt0) cc_final: 0.8207 (tt0) REVERT: C 855 PHE cc_start: 0.8534 (m-10) cc_final: 0.8231 (m-80) REVERT: C 856 ASN cc_start: 0.9184 (m110) cc_final: 0.8773 (m-40) REVERT: C 923 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9171 (mp) REVERT: C 957 GLN cc_start: 0.8774 (tt0) cc_final: 0.8551 (tt0) REVERT: C 984 LEU cc_start: 0.8191 (tt) cc_final: 0.7903 (tt) REVERT: C 988 GLU cc_start: 0.8983 (mp0) cc_final: 0.8545 (tp30) REVERT: C 1017 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8819 (tm-30) REVERT: C 1092 GLU cc_start: 0.8513 (pm20) cc_final: 0.8250 (pm20) outliers start: 48 outliers final: 37 residues processed: 242 average time/residue: 0.1399 time to fit residues: 55.7750 Evaluate side-chains 224 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 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 303 LEU 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 997 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 131 CYS 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 565 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 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 375 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1017 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 57 optimal weight: 0.8980 chunk 230 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.104410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067553 restraints weight = 53167.980| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.25 r_work: 0.2930 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.7510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 22844 Z= 0.188 Angle : 0.603 11.977 31183 Z= 0.306 Chirality : 0.045 0.192 3703 Planarity : 0.004 0.048 3920 Dihedral : 5.213 53.919 4085 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.07 % Allowed : 16.63 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.16), residues: 2699 helix: 2.22 (0.19), residues: 666 sheet: -0.03 (0.19), residues: 636 loop : -0.22 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 995 TYR 0.021 0.001 TYR A1067 PHE 0.024 0.001 PHE B 823 TRP 0.034 0.002 TRP A 104 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00430 (22755) covalent geometry : angle 0.58977 (30950) SS BOND : bond 0.00192 ( 34) SS BOND : angle 1.63408 ( 68) hydrogen bonds : bond 0.03891 ( 985) hydrogen bonds : angle 5.24537 ( 2868) link_BETA1-4 : bond 0.00237 ( 18) link_BETA1-4 : angle 1.05239 ( 54) link_NAG-ASN : bond 0.00341 ( 37) link_NAG-ASN : angle 1.76736 ( 111) *********************** 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 239 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8719 (mm) cc_final: 0.8313 (tp) REVERT: A 200 TYR cc_start: 0.7901 (m-80) cc_final: 0.7459 (m-80) REVERT: A 214 ARG cc_start: 0.6975 (tpt-90) cc_final: 0.6753 (tpt-90) REVERT: A 748 GLU cc_start: 0.9147 (mp0) cc_final: 0.8928 (mp0) REVERT: A 754 LEU cc_start: 0.9446 (mp) cc_final: 0.9234 (mp) REVERT: A 759 PHE cc_start: 0.8703 (m-80) cc_final: 0.8314 (m-80) REVERT: A 955 ASN cc_start: 0.8669 (m-40) cc_final: 0.8367 (t0) REVERT: A 988 GLU cc_start: 0.9139 (mp0) cc_final: 0.8747 (pm20) REVERT: A 995 ARG cc_start: 0.9202 (mtp-110) cc_final: 0.8490 (mtp85) REVERT: B 55 PHE cc_start: 0.8153 (m-80) cc_final: 0.7672 (m-80) REVERT: B 170 TYR cc_start: 0.8021 (t80) cc_final: 0.7625 (t80) REVERT: B 177 MET cc_start: 0.7338 (pmm) cc_final: 0.7043 (pmm) REVERT: B 242 LEU cc_start: 0.8120 (mm) cc_final: 0.7542 (mp) REVERT: B 269 TYR cc_start: 0.7714 (m-10) cc_final: 0.7341 (m-10) REVERT: B 571 ASP cc_start: 0.8623 (m-30) cc_final: 0.8333 (t0) REVERT: B 725 GLU cc_start: 0.8900 (tt0) cc_final: 0.8656 (tt0) REVERT: B 755 GLN cc_start: 0.9160 (mt0) cc_final: 0.8858 (tt0) REVERT: B 988 GLU cc_start: 0.9230 (tp30) cc_final: 0.8835 (tp30) REVERT: C 52 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8380 (tm-30) REVERT: C 324 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7945 (pm20) REVERT: C 423 TYR cc_start: 0.5653 (t80) cc_final: 0.5427 (t80) REVERT: C 572 THR cc_start: 0.7680 (m) cc_final: 0.7394 (p) REVERT: C 773 GLU cc_start: 0.8696 (tt0) cc_final: 0.8340 (tt0) REVERT: C 855 PHE cc_start: 0.8529 (m-10) cc_final: 0.8217 (m-80) REVERT: C 856 ASN cc_start: 0.9222 (m110) cc_final: 0.8844 (m-40) REVERT: C 923 ILE cc_start: 0.9617 (OUTLIER) cc_final: 0.9361 (mp) REVERT: C 957 GLN cc_start: 0.8851 (tt0) cc_final: 0.8645 (tt0) REVERT: C 988 GLU cc_start: 0.8918 (mp0) cc_final: 0.8542 (tp30) REVERT: C 1017 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8953 (tm-30) outliers start: 50 outliers final: 39 residues processed: 229 average time/residue: 0.1412 time to fit residues: 52.8674 Evaluate side-chains 224 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU 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 997 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 131 CYS 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 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN 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 131 CYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1017 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 241 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 103 optimal weight: 0.0050 chunk 189 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 246 optimal weight: 0.8980 chunk 234 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.105656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.068759 restraints weight = 53032.693| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.40 r_work: 0.2945 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.7570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 22844 Z= 0.131 Angle : 0.591 12.817 31183 Z= 0.300 Chirality : 0.044 0.231 3703 Planarity : 0.004 0.047 3920 Dihedral : 5.109 54.645 4085 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.82 % Allowed : 16.92 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.16), residues: 2699 helix: 2.21 (0.19), residues: 667 sheet: 0.05 (0.19), residues: 630 loop : -0.17 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 346 TYR 0.022 0.001 TYR B 170 PHE 0.025 0.001 PHE C 347 TRP 0.038 0.002 TRP A 104 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00299 (22755) covalent geometry : angle 0.57976 (30950) SS BOND : bond 0.00178 ( 34) SS BOND : angle 1.45009 ( 68) hydrogen bonds : bond 0.03649 ( 985) hydrogen bonds : angle 5.13914 ( 2868) link_BETA1-4 : bond 0.00321 ( 18) link_BETA1-4 : angle 0.95379 ( 54) link_NAG-ASN : bond 0.00246 ( 37) link_NAG-ASN : angle 1.62815 ( 111) ********************** 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 235 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8721 (mm) cc_final: 0.8326 (tp) REVERT: A 99 ASN cc_start: 0.8378 (m-40) cc_final: 0.7633 (p0) REVERT: A 200 TYR cc_start: 0.7914 (m-80) cc_final: 0.7487 (m-80) REVERT: A 214 ARG cc_start: 0.7029 (tpt-90) cc_final: 0.6816 (tpt-90) REVERT: A 748 GLU cc_start: 0.9196 (mp0) cc_final: 0.8984 (mp0) REVERT: A 754 LEU cc_start: 0.9431 (mp) cc_final: 0.9228 (mp) REVERT: A 759 PHE cc_start: 0.8648 (m-80) cc_final: 0.8192 (m-80) REVERT: A 955 ASN cc_start: 0.8703 (m-40) cc_final: 0.8262 (t0) REVERT: A 988 GLU cc_start: 0.9068 (mp0) cc_final: 0.8694 (pm20) REVERT: A 995 ARG cc_start: 0.9175 (mtp-110) cc_final: 0.8696 (mtp85) REVERT: B 55 PHE cc_start: 0.8169 (m-80) cc_final: 0.7607 (m-80) REVERT: B 170 TYR cc_start: 0.7986 (t80) cc_final: 0.7605 (t80) REVERT: B 177 MET cc_start: 0.7145 (pmm) cc_final: 0.6810 (pmm) REVERT: B 242 LEU cc_start: 0.8196 (mm) cc_final: 0.7665 (mp) REVERT: B 269 TYR cc_start: 0.7715 (m-10) cc_final: 0.7257 (m-10) REVERT: B 571 ASP cc_start: 0.8612 (m-30) cc_final: 0.8337 (t0) REVERT: B 725 GLU cc_start: 0.8901 (tt0) cc_final: 0.8601 (tt0) REVERT: B 755 GLN cc_start: 0.9165 (mt0) cc_final: 0.8869 (tt0) REVERT: C 52 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8363 (tm-30) REVERT: C 324 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7957 (pm20) REVERT: C 423 TYR cc_start: 0.5312 (t80) cc_final: 0.5060 (t80) REVERT: C 572 THR cc_start: 0.7618 (m) cc_final: 0.7352 (p) REVERT: C 773 GLU cc_start: 0.8641 (tt0) cc_final: 0.8255 (tt0) REVERT: C 855 PHE cc_start: 0.8555 (m-10) cc_final: 0.8232 (m-80) REVERT: C 856 ASN cc_start: 0.9208 (m110) cc_final: 0.8787 (m-40) REVERT: C 923 ILE cc_start: 0.9522 (OUTLIER) cc_final: 0.9253 (mp) REVERT: C 950 ASP cc_start: 0.8840 (m-30) cc_final: 0.8378 (m-30) REVERT: C 957 GLN cc_start: 0.8805 (tt0) cc_final: 0.8578 (tt0) REVERT: C 988 GLU cc_start: 0.8998 (mp0) cc_final: 0.8573 (tp30) outliers start: 44 outliers final: 38 residues processed: 226 average time/residue: 0.1363 time to fit residues: 50.6520 Evaluate side-chains 225 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 131 CYS 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 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 785 VAL 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 51 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 489 TYR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 150 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 208 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 169 optimal weight: 0.6980 chunk 214 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1010 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.105472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.068708 restraints weight = 53104.125| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.38 r_work: 0.2945 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.7650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22844 Z= 0.136 Angle : 0.587 12.777 31183 Z= 0.298 Chirality : 0.044 0.219 3703 Planarity : 0.004 0.048 3920 Dihedral : 5.003 54.297 4085 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.90 % Allowed : 17.05 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.16), residues: 2699 helix: 2.27 (0.19), residues: 668 sheet: 0.07 (0.19), residues: 632 loop : -0.17 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1014 TYR 0.022 0.001 TYR B 170 PHE 0.024 0.001 PHE B 823 TRP 0.037 0.002 TRP A 104 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00310 (22755) covalent geometry : angle 0.57618 (30950) SS BOND : bond 0.00185 ( 34) SS BOND : angle 1.38517 ( 68) hydrogen bonds : bond 0.03615 ( 985) hydrogen bonds : angle 5.08207 ( 2868) link_BETA1-4 : bond 0.00279 ( 18) link_BETA1-4 : angle 0.98451 ( 54) link_NAG-ASN : bond 0.00244 ( 37) link_NAG-ASN : angle 1.60197 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5909.51 seconds wall clock time: 101 minutes 53.89 seconds (6113.89 seconds total)