Starting phenix.real_space_refine on Thu Mar 5 16:38:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q1z_13776/03_2026/7q1z_13776.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q1z_13776/03_2026/7q1z_13776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q1z_13776/03_2026/7q1z_13776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q1z_13776/03_2026/7q1z_13776.map" model { file = "/net/cci-nas-00/data/ceres_data/7q1z_13776/03_2026/7q1z_13776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q1z_13776/03_2026/7q1z_13776.cif" } resolution = 3.4 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= 0.016 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 99 5.16 5 C 15087 2.51 5 N 3849 2.21 5 O 4659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23694 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "B" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "C" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.61, per 1000 atoms: 0.24 Number of scatterers: 23694 At special positions: 0 Unit cell: (136.85, 135.7, 171.35, 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 99 16.00 O 4659 8.00 N 3849 7.00 C 15087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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=3, 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 822.8 milliseconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 44 sheets defined 26.5% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.381A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.697A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 501 through 501 No H-bonds generated for 'chain 'A' and resid 501 through 501' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' 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 removed outlier: 3.589A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.123A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 945 removed outlier: 3.853A pdb=" N LEU A 945 " --> pdb=" O ALA A 942 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 942 through 945' Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.688A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.417A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.109A 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 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.400A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.532A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.794A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 501 No H-bonds generated for 'chain 'B' and resid 501 through 501' Processing helix chain 'B' and resid 503 through 506 Processing helix chain 'B' and resid 737 through 744 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: 3.555A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.125A 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 946 through 965 removed outlier: 3.716A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.223A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.066A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.447A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.636A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.346A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 501 No H-bonds generated for 'chain 'C' and resid 501 through 501' Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' 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: 3.565A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.523A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.102A 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 946 through 965 removed outlier: 3.670A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.458A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.109A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.679A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.564A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.459A 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: 3.679A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.852A 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 removed outlier: 6.157A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.768A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.139A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.410A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.823A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.025A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.901A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.782A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.432A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.856A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.719A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.853A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.210A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.908A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.192A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.526A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.445A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.525A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.053A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 removed outlier: 4.033A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.770A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.799A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.441A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.030A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.646A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.628A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.236A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.841A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.977A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.985A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.457A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.143A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.812A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.840A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.461A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.010A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 994 hydrogen bonds defined for protein. 2748 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: 5.51 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7489 1.35 - 1.47: 6158 1.47 - 1.59: 10428 1.59 - 1.72: 0 1.72 - 1.84: 123 Bond restraints: 24198 Sorted by residual: bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.40e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 ... (remaining 24193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 31600 1.42 - 2.83: 1157 2.83 - 4.25: 125 4.25 - 5.66: 20 5.66 - 7.08: 11 Bond angle restraints: 32913 Sorted by residual: angle pdb=" C ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " ideal model delta sigma weight residual 116.63 110.07 6.56 1.16e+00 7.43e-01 3.20e+01 angle pdb=" C ASN C 87 " pdb=" CA ASN C 87 " pdb=" CB ASN C 87 " ideal model delta sigma weight residual 117.23 110.15 7.08 1.36e+00 5.41e-01 2.71e+01 angle pdb=" C ASN B 87 " pdb=" CA ASN B 87 " pdb=" CB ASN B 87 " ideal model delta sigma weight residual 117.23 110.22 7.01 1.36e+00 5.41e-01 2.65e+01 angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 117.23 110.23 7.00 1.36e+00 5.41e-01 2.65e+01 angle pdb=" C PHE C 32 " pdb=" CA PHE C 32 " pdb=" CB PHE C 32 " ideal model delta sigma weight residual 117.23 110.32 6.91 1.36e+00 5.41e-01 2.58e+01 ... (remaining 32908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 14159 17.91 - 35.82: 797 35.82 - 53.73: 184 53.73 - 71.64: 61 71.64 - 89.55: 27 Dihedral angle restraints: 15228 sinusoidal: 6738 harmonic: 8490 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.30 -86.30 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.29 -86.29 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.13 -86.13 1 1.00e+01 1.00e-02 8.95e+01 ... (remaining 15225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2695 0.040 - 0.079: 828 0.079 - 0.119: 379 0.119 - 0.159: 26 0.159 - 0.198: 4 Chirality restraints: 3932 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.84e-01 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 3929 not shown) Planarity restraints: 4196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " -0.076 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO C 82 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 81 " -0.071 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO B 82 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 881 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C THR C 881 " -0.027 2.00e-02 2.50e+03 pdb=" O THR C 881 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE C 882 " 0.009 2.00e-02 2.50e+03 ... (remaining 4193 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 208 2.64 - 3.20: 20839 3.20 - 3.77: 34683 3.77 - 4.33: 49720 4.33 - 4.90: 82833 Nonbonded interactions: 188283 Sorted by model distance: nonbonded pdb=" OG1 THR A 393 " pdb=" OE2 GLU A 516 " model vdw 2.074 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" OD2 ASP C 53 " model vdw 2.229 3.040 nonbonded pdb=" NZ LYS C 557 " pdb=" OD2 ASP C 574 " model vdw 2.233 3.120 nonbonded pdb=" OG SER A 596 " pdb=" OE1 GLN A 613 " model vdw 2.236 3.040 ... (remaining 188278 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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' } 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: 5.230 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 22.060 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3130 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 : 0.004 0.050 24284 Z= 0.199 Angle : 0.617 7.081 33126 Z= 0.338 Chirality : 0.045 0.198 3932 Planarity : 0.004 0.113 4164 Dihedral : 12.724 89.552 9636 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.04 % Allowed : 0.31 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.15), residues: 2844 helix: 1.52 (0.20), residues: 723 sheet: 0.38 (0.19), residues: 645 loop : -0.08 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1019 TYR 0.018 0.001 TYR A 453 PHE 0.018 0.001 PHE B 817 TRP 0.012 0.001 TRP A 886 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00419 (24198) covalent geometry : angle 0.60657 (32913) SS BOND : bond 0.00455 ( 36) SS BOND : angle 1.17292 ( 72) hydrogen bonds : bond 0.17339 ( 988) hydrogen bonds : angle 7.63170 ( 2748) Misc. bond : bond 0.00024 ( 3) link_BETA1-4 : bond 0.00314 ( 15) link_BETA1-4 : angle 1.25037 ( 45) link_NAG-ASN : bond 0.00260 ( 32) link_NAG-ASN : angle 1.87734 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 342 time to evaluate : 0.653 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 905 ARG cc_start: 0.2715 (mmt180) cc_final: 0.2191 (mtm180) REVERT: B 194 PHE cc_start: 0.4663 (m-80) cc_final: 0.3487 (m-10) REVERT: B 224 GLU cc_start: 0.5431 (pm20) cc_final: 0.4723 (mp0) REVERT: B 299 THR cc_start: 0.5027 (p) cc_final: 0.3050 (m) REVERT: B 358 ILE cc_start: 0.5281 (mt) cc_final: 0.4269 (mt) REVERT: B 394 ASN cc_start: 0.5133 (OUTLIER) cc_final: 0.4753 (m-40) REVERT: B 543 PHE cc_start: 0.4419 (m-80) cc_final: 0.2319 (m-10) REVERT: B 741 TYR cc_start: 0.2910 (t80) cc_final: 0.2362 (t80) REVERT: B 992 GLN cc_start: 0.3088 (mm-40) cc_final: 0.2704 (mm110) REVERT: C 281 GLU cc_start: 0.5233 (tp30) cc_final: 0.4937 (mm-30) REVERT: C 513 LEU cc_start: 0.5000 (mt) cc_final: 0.4737 (mt) REVERT: C 1018 ILE cc_start: 0.4296 (mm) cc_final: 0.4005 (tp) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.1695 time to fit residues: 90.4189 Evaluate side-chains 269 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.1980 chunk 111 optimal weight: 4.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 556 ASN A 655 HIS A 675 GLN A 764 ASN A 955 ASN B 134 GLN B 394 ASN B 536 ASN B 613 GLN B 675 GLN B 901 GLN B 925 ASN B 949 GLN B1023 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 196 ASN C 394 ASN C 501 ASN C 613 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C1088 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.167082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136964 restraints weight = 37225.130| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.94 r_work: 0.3526 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4959 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.138 24284 Z= 0.310 Angle : 0.987 26.048 33126 Z= 0.485 Chirality : 0.057 0.732 3932 Planarity : 0.007 0.087 4164 Dihedral : 7.166 59.480 4424 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 1.84 % Allowed : 6.30 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 2844 helix: 0.44 (0.19), residues: 726 sheet: 0.20 (0.21), residues: 576 loop : -0.64 (0.14), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1039 TYR 0.053 0.003 TYR B 380 PHE 0.039 0.004 PHE A 543 TRP 0.019 0.003 TRP B1102 HIS 0.006 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00655 (24198) covalent geometry : angle 0.95960 (32913) SS BOND : bond 0.01159 ( 36) SS BOND : angle 1.60977 ( 72) hydrogen bonds : bond 0.05272 ( 988) hydrogen bonds : angle 6.46112 ( 2748) Misc. bond : bond 0.00073 ( 3) link_BETA1-4 : bond 0.01050 ( 15) link_BETA1-4 : angle 2.00356 ( 45) link_NAG-ASN : bond 0.01051 ( 32) link_NAG-ASN : angle 4.05003 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 415 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ILE cc_start: 0.5060 (OUTLIER) cc_final: 0.4841 (pt) REVERT: A 312 ILE cc_start: 0.4638 (OUTLIER) cc_final: 0.4380 (tt) REVERT: A 327 VAL cc_start: 0.5871 (t) cc_final: 0.5320 (p) REVERT: A 516 GLU cc_start: 0.5785 (pp20) cc_final: 0.5441 (mp0) REVERT: A 748 GLU cc_start: 0.6706 (mp0) cc_final: 0.6504 (mp0) REVERT: A 764 ASN cc_start: 0.6878 (m110) cc_final: 0.6575 (m110) REVERT: A 906 PHE cc_start: 0.6001 (m-80) cc_final: 0.5187 (m-80) REVERT: A 970 PHE cc_start: 0.6201 (m-80) cc_final: 0.4812 (m-10) REVERT: A 988 GLU cc_start: 0.6901 (pm20) cc_final: 0.6464 (pm20) REVERT: A 1000 ARG cc_start: 0.6796 (mtt180) cc_final: 0.5792 (ttm170) REVERT: A 1067 TYR cc_start: 0.6168 (t80) cc_final: 0.5822 (t80) REVERT: B 30 ASN cc_start: 0.4127 (t0) cc_final: 0.3811 (p0) REVERT: B 121 ASN cc_start: 0.5684 (OUTLIER) cc_final: 0.4953 (p0) REVERT: B 224 GLU cc_start: 0.5893 (pm20) cc_final: 0.5459 (mp0) REVERT: B 285 ILE cc_start: 0.6653 (mt) cc_final: 0.6347 (mt) REVERT: B 394 ASN cc_start: 0.7015 (OUTLIER) cc_final: 0.6795 (p0) REVERT: B 900 MET cc_start: 0.4940 (mmt) cc_final: 0.4661 (mmp) REVERT: B 1000 ARG cc_start: 0.5290 (mpt180) cc_final: 0.4208 (mtt90) REVERT: C 239 GLN cc_start: 0.6317 (tp-100) cc_final: 0.5983 (tp40) REVERT: C 269 TYR cc_start: 0.6676 (m-80) cc_final: 0.6453 (m-80) REVERT: C 273 ARG cc_start: 0.7033 (mtp85) cc_final: 0.6700 (mmm160) REVERT: C 568 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.7007 (p0) REVERT: C 768 THR cc_start: 0.6839 (m) cc_final: 0.5605 (p) REVERT: C 777 ASN cc_start: 0.5151 (m-40) cc_final: 0.4914 (m-40) REVERT: C 963 VAL cc_start: 0.6354 (t) cc_final: 0.5481 (p) REVERT: C 1004 LEU cc_start: 0.5573 (OUTLIER) cc_final: 0.4822 (mt) REVERT: C 1008 VAL cc_start: 0.5625 (t) cc_final: 0.4436 (m) REVERT: C 1029 MET cc_start: 0.6388 (tmm) cc_final: 0.6135 (tmm) outliers start: 47 outliers final: 20 residues processed: 437 average time/residue: 0.1596 time to fit residues: 108.8056 Evaluate side-chains 353 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 327 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 248 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 244 optimal weight: 0.0470 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 170 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 196 ASN A 409 GLN A 603 ASN A 655 HIS A1048 HIS B 30 ASN B 317 ASN B 774 GLN B 901 GLN B 957 GLN B 992 GLN B1058 HIS ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.168911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139028 restraints weight = 37446.436| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.98 r_work: 0.3573 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.7760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.160 24284 Z= 0.320 Angle : 0.991 25.910 33126 Z= 0.499 Chirality : 0.057 0.571 3932 Planarity : 0.007 0.131 4164 Dihedral : 7.745 134.369 4424 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 3.48 % Allowed : 9.47 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 2844 helix: 0.31 (0.19), residues: 732 sheet: 0.13 (0.21), residues: 555 loop : -0.96 (0.14), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 646 TYR 0.035 0.003 TYR C1067 PHE 0.032 0.003 PHE B 802 TRP 0.045 0.003 TRP C 104 HIS 0.012 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00696 (24198) covalent geometry : angle 0.94351 (32913) SS BOND : bond 0.01303 ( 36) SS BOND : angle 3.62448 ( 72) hydrogen bonds : bond 0.06529 ( 988) hydrogen bonds : angle 6.48649 ( 2748) Misc. bond : bond 0.03645 ( 3) link_BETA1-4 : bond 0.00685 ( 15) link_BETA1-4 : angle 1.60071 ( 45) link_NAG-ASN : bond 0.02124 ( 32) link_NAG-ASN : angle 4.74816 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 513 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7113 (p90) cc_final: 0.6826 (p90) REVERT: A 355 ARG cc_start: 0.7103 (ttm170) cc_final: 0.6686 (ttm-80) REVERT: A 512 VAL cc_start: 0.7337 (t) cc_final: 0.7057 (t) REVERT: A 515 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.7389 (m-80) REVERT: A 697 MET cc_start: 0.5302 (ppp) cc_final: 0.4611 (ptm) REVERT: A 714 ILE cc_start: 0.6957 (OUTLIER) cc_final: 0.6510 (mt) REVERT: A 729 VAL cc_start: 0.7905 (t) cc_final: 0.6928 (p) REVERT: A 732 THR cc_start: 0.8143 (m) cc_final: 0.7913 (p) REVERT: A 748 GLU cc_start: 0.7354 (mp0) cc_final: 0.7125 (mp0) REVERT: A 868 GLU cc_start: 0.6959 (mp0) cc_final: 0.6521 (mp0) REVERT: A 869 MET cc_start: 0.8020 (ttp) cc_final: 0.7642 (ttm) REVERT: A 934 ILE cc_start: 0.7309 (mm) cc_final: 0.6941 (mt) REVERT: A 990 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7461 (tm-30) REVERT: A 1008 VAL cc_start: 0.8443 (p) cc_final: 0.8057 (t) REVERT: A 1120 THR cc_start: 0.6410 (p) cc_final: 0.5946 (t) REVERT: B 285 ILE cc_start: 0.7842 (mt) cc_final: 0.7590 (mm) REVERT: B 382 VAL cc_start: 0.7741 (m) cc_final: 0.7500 (t) REVERT: B 428 ASP cc_start: 0.6268 (t0) cc_final: 0.5939 (t0) REVERT: B 514 SER cc_start: 0.7990 (t) cc_final: 0.7396 (p) REVERT: B 858 LEU cc_start: 0.8180 (tt) cc_final: 0.7871 (mp) REVERT: B 987 PRO cc_start: 0.8010 (Cg_exo) cc_final: 0.7802 (Cg_endo) REVERT: B 988 GLU cc_start: 0.7308 (mp0) cc_final: 0.7041 (mp0) REVERT: B 990 GLU cc_start: 0.7421 (tt0) cc_final: 0.6666 (tt0) REVERT: B 994 ASP cc_start: 0.6971 (m-30) cc_final: 0.6481 (m-30) REVERT: B 998 THR cc_start: 0.7775 (m) cc_final: 0.7543 (p) REVERT: B 1000 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7385 (mmt90) REVERT: B 1009 THR cc_start: 0.8296 (m) cc_final: 0.7795 (m) REVERT: B 1023 ASN cc_start: 0.6849 (m-40) cc_final: 0.6622 (m-40) REVERT: B 1050 MET cc_start: 0.6167 (pmm) cc_final: 0.5738 (ptp) REVERT: B 1081 ILE cc_start: 0.6228 (OUTLIER) cc_final: 0.5890 (mt) REVERT: C 53 ASP cc_start: 0.5381 (t70) cc_final: 0.4661 (t70) REVERT: C 191 GLU cc_start: 0.6878 (tt0) cc_final: 0.6607 (tt0) REVERT: C 273 ARG cc_start: 0.6904 (mtp85) cc_final: 0.6592 (mtp180) REVERT: C 365 TYR cc_start: 0.7481 (m-80) cc_final: 0.7095 (m-80) REVERT: C 537 LYS cc_start: 0.7502 (ttpt) cc_final: 0.7165 (ttpt) REVERT: C 560 LEU cc_start: 0.6202 (mt) cc_final: 0.5955 (mt) REVERT: C 599 THR cc_start: 0.8049 (t) cc_final: 0.7818 (t) REVERT: C 772 VAL cc_start: 0.6927 (t) cc_final: 0.5874 (m) REVERT: C 868 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6969 (tm-30) REVERT: C 902 MET cc_start: 0.6836 (mmp) cc_final: 0.6508 (mmp) REVERT: C 996 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7234 (mt) REVERT: C 1014 ARG cc_start: 0.7647 (ttp-110) cc_final: 0.7405 (ttm-80) REVERT: C 1029 MET cc_start: 0.7237 (tmm) cc_final: 0.6855 (tpp) REVERT: C 1102 TRP cc_start: 0.6208 (m100) cc_final: 0.5988 (m100) outliers start: 89 outliers final: 30 residues processed: 564 average time/residue: 0.1542 time to fit residues: 137.1819 Evaluate side-chains 458 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 423 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 236 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 268 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 289 optimal weight: 0.7980 chunk 288 optimal weight: 0.3980 chunk 128 optimal weight: 0.5980 chunk 285 optimal weight: 0.9980 chunk 132 optimal weight: 30.0000 chunk 91 optimal weight: 0.6980 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 207 HIS A 409 GLN A 613 GLN A 764 ASN A 901 GLN A 919 ASN A1048 HIS A1064 HIS A1119 ASN B 49 HIS B 196 ASN B 314 GLN B 370 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN B 901 GLN B 914 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1002 GLN B1108 ASN C 196 ASN C 603 ASN C 607 GLN C 764 ASN C 784 GLN C 804 GLN C 901 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.167898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.137175 restraints weight = 37216.941| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.02 r_work: 0.3544 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 1.0047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 24284 Z= 0.248 Angle : 0.863 20.033 33126 Z= 0.426 Chirality : 0.055 1.076 3932 Planarity : 0.007 0.142 4164 Dihedral : 6.412 57.810 4422 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.72 % Allowed : 13.97 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 2844 helix: 0.56 (0.19), residues: 732 sheet: -0.04 (0.20), residues: 621 loop : -0.89 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 357 TYR 0.032 0.002 TYR B1067 PHE 0.030 0.003 PHE C 888 TRP 0.014 0.002 TRP C 64 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00554 (24198) covalent geometry : angle 0.82569 (32913) SS BOND : bond 0.01469 ( 36) SS BOND : angle 3.09455 ( 72) hydrogen bonds : bond 0.04881 ( 988) hydrogen bonds : angle 6.05207 ( 2748) Misc. bond : bond 0.03507 ( 3) link_BETA1-4 : bond 0.00508 ( 15) link_BETA1-4 : angle 1.42311 ( 45) link_NAG-ASN : bond 0.00918 ( 32) link_NAG-ASN : angle 3.89052 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 536 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6743 (tp40) cc_final: 0.6387 (tp40) REVERT: A 105 ILE cc_start: 0.7441 (pt) cc_final: 0.7214 (mt) REVERT: A 354 ASN cc_start: 0.7695 (t0) cc_final: 0.7399 (t0) REVERT: A 515 PHE cc_start: 0.8155 (m-80) cc_final: 0.7907 (m-10) REVERT: A 537 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8195 (mttp) REVERT: A 583 GLU cc_start: 0.6533 (mm-30) cc_final: 0.5905 (mm-30) REVERT: A 599 THR cc_start: 0.6991 (t) cc_final: 0.6765 (t) REVERT: A 673 SER cc_start: 0.8679 (OUTLIER) cc_final: 0.8325 (t) REVERT: A 859 THR cc_start: 0.8205 (p) cc_final: 0.7957 (t) REVERT: A 869 MET cc_start: 0.8413 (ttp) cc_final: 0.7840 (mtm) REVERT: A 985 ASP cc_start: 0.7580 (p0) cc_final: 0.7058 (p0) REVERT: A 995 ARG cc_start: 0.8373 (tpp80) cc_final: 0.8111 (ttm-80) REVERT: A 1002 GLN cc_start: 0.8606 (tp40) cc_final: 0.8091 (tm-30) REVERT: A 1023 ASN cc_start: 0.8178 (t0) cc_final: 0.7538 (m-40) REVERT: A 1050 MET cc_start: 0.8226 (ptp) cc_final: 0.8019 (ptp) REVERT: A 1129 VAL cc_start: 0.7643 (OUTLIER) cc_final: 0.7272 (m) REVERT: B 224 GLU cc_start: 0.6395 (pm20) cc_final: 0.4984 (mp0) REVERT: B 239 GLN cc_start: 0.7815 (tt0) cc_final: 0.7488 (tm-30) REVERT: B 240 THR cc_start: 0.7761 (m) cc_final: 0.7340 (t) REVERT: B 305 SER cc_start: 0.8645 (t) cc_final: 0.8294 (p) REVERT: B 394 ASN cc_start: 0.7899 (p0) cc_final: 0.7676 (p0) REVERT: B 514 SER cc_start: 0.8251 (t) cc_final: 0.7686 (p) REVERT: B 752 LEU cc_start: 0.7668 (mt) cc_final: 0.7456 (mt) REVERT: B 858 LEU cc_start: 0.8639 (tt) cc_final: 0.8436 (mp) REVERT: B 900 MET cc_start: 0.6974 (mmt) cc_final: 0.6676 (mmm) REVERT: B 902 MET cc_start: 0.5254 (OUTLIER) cc_final: 0.4889 (ttt) REVERT: B 987 PRO cc_start: 0.8606 (Cg_exo) cc_final: 0.8291 (Cg_endo) REVERT: B 988 GLU cc_start: 0.7723 (mp0) cc_final: 0.7503 (mp0) REVERT: B 990 GLU cc_start: 0.7696 (tt0) cc_final: 0.7484 (tt0) REVERT: B 1000 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7656 (mtt90) REVERT: B 1030 SER cc_start: 0.7783 (m) cc_final: 0.7378 (p) REVERT: B 1045 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6791 (ttpp) REVERT: B 1123 SER cc_start: 0.7114 (t) cc_final: 0.6858 (t) REVERT: C 191 GLU cc_start: 0.7333 (tt0) cc_final: 0.6748 (tt0) REVERT: C 279 TYR cc_start: 0.7690 (m-80) cc_final: 0.7405 (m-10) REVERT: C 365 TYR cc_start: 0.7187 (m-80) cc_final: 0.6644 (m-80) REVERT: C 386 LYS cc_start: 0.8338 (mtpp) cc_final: 0.8089 (mmtt) REVERT: C 513 LEU cc_start: 0.7543 (mt) cc_final: 0.7258 (mt) REVERT: C 515 PHE cc_start: 0.8204 (m-80) cc_final: 0.7986 (m-10) REVERT: C 516 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.6020 (tt0) REVERT: C 556 ASN cc_start: 0.7424 (p0) cc_final: 0.6994 (p0) REVERT: C 595 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8539 (t) REVERT: C 603 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7921 (t0) REVERT: C 651 ILE cc_start: 0.8150 (mt) cc_final: 0.7903 (mm) REVERT: C 756 TYR cc_start: 0.8105 (m-80) cc_final: 0.7466 (m-80) REVERT: C 778 THR cc_start: 0.7537 (m) cc_final: 0.6421 (p) REVERT: C 868 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7227 (tp30) REVERT: C 872 GLN cc_start: 0.7273 (tp40) cc_final: 0.6880 (tt0) REVERT: C 902 MET cc_start: 0.7360 (mmp) cc_final: 0.6827 (mmm) REVERT: C 984 LEU cc_start: 0.7768 (mt) cc_final: 0.7454 (mp) REVERT: C 994 ASP cc_start: 0.7682 (m-30) cc_final: 0.7440 (m-30) REVERT: C 995 ARG cc_start: 0.7780 (mtt90) cc_final: 0.7546 (mtt90) REVERT: C 1014 ARG cc_start: 0.8086 (ttp-110) cc_final: 0.7790 (ttm-80) REVERT: C 1111 GLU cc_start: 0.7845 (tt0) cc_final: 0.7587 (tm-30) outliers start: 95 outliers final: 47 residues processed: 586 average time/residue: 0.1583 time to fit residues: 147.3996 Evaluate side-chains 503 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 448 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 253 optimal weight: 0.6980 chunk 282 optimal weight: 0.9980 chunk 134 optimal weight: 0.4980 chunk 266 optimal weight: 0.2980 chunk 281 optimal weight: 0.0980 chunk 172 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 13 optimal weight: 0.0370 chunk 284 optimal weight: 0.5980 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 394 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 955 ASN A1048 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 901 GLN B 914 ASN B 949 GLN B1023 ASN B1048 HIS C 52 GLN C 603 ASN C 710 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C 955 ASN C 969 ASN C1002 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.167190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.136486 restraints weight = 36937.349| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.01 r_work: 0.3526 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 1.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24284 Z= 0.148 Angle : 0.672 21.713 33126 Z= 0.338 Chirality : 0.046 0.316 3932 Planarity : 0.004 0.054 4164 Dihedral : 5.837 59.575 4422 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.40 % Allowed : 16.74 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 2844 helix: 1.05 (0.20), residues: 738 sheet: 0.22 (0.21), residues: 609 loop : -0.76 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 567 TYR 0.022 0.001 TYR B1067 PHE 0.022 0.002 PHE C 32 TRP 0.012 0.001 TRP B1102 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00332 (24198) covalent geometry : angle 0.62858 (32913) SS BOND : bond 0.01107 ( 36) SS BOND : angle 2.72138 ( 72) hydrogen bonds : bond 0.04153 ( 988) hydrogen bonds : angle 5.72439 ( 2748) Misc. bond : bond 0.00021 ( 3) link_BETA1-4 : bond 0.00427 ( 15) link_BETA1-4 : angle 1.31906 ( 45) link_NAG-ASN : bond 0.00824 ( 32) link_NAG-ASN : angle 3.76775 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 464 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6842 (tp40) cc_final: 0.6544 (tp40) REVERT: A 329 PHE cc_start: 0.7133 (m-80) cc_final: 0.6904 (m-10) REVERT: A 354 ASN cc_start: 0.7796 (t0) cc_final: 0.7410 (t0) REVERT: A 537 LYS cc_start: 0.8310 (mtmm) cc_final: 0.8009 (mtpp) REVERT: A 578 ASP cc_start: 0.7120 (t0) cc_final: 0.6893 (t0) REVERT: A 608 VAL cc_start: 0.7616 (t) cc_final: 0.7332 (p) REVERT: A 673 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8360 (p) REVERT: A 714 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7638 (mt) REVERT: A 729 VAL cc_start: 0.8511 (t) cc_final: 0.8135 (m) REVERT: A 773 GLU cc_start: 0.8171 (tp30) cc_final: 0.7769 (tp30) REVERT: A 878 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7902 (tp) REVERT: A 1002 GLN cc_start: 0.8510 (tp40) cc_final: 0.8071 (tm-30) REVERT: A 1023 ASN cc_start: 0.8140 (t0) cc_final: 0.7673 (m-40) REVERT: B 224 GLU cc_start: 0.6424 (pm20) cc_final: 0.5293 (mp0) REVERT: B 239 GLN cc_start: 0.7796 (tt0) cc_final: 0.7414 (tm-30) REVERT: B 240 THR cc_start: 0.7712 (m) cc_final: 0.7321 (t) REVERT: B 305 SER cc_start: 0.8657 (t) cc_final: 0.8320 (p) REVERT: B 306 PHE cc_start: 0.7923 (t80) cc_final: 0.7587 (t80) REVERT: B 428 ASP cc_start: 0.6538 (t0) cc_final: 0.6160 (t0) REVERT: B 514 SER cc_start: 0.8255 (t) cc_final: 0.7623 (p) REVERT: B 735 SER cc_start: 0.8693 (p) cc_final: 0.8344 (t) REVERT: B 752 LEU cc_start: 0.7806 (mt) cc_final: 0.7585 (mt) REVERT: B 765 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7347 (ttm110) REVERT: B 900 MET cc_start: 0.6938 (mmt) cc_final: 0.6676 (mmm) REVERT: B 916 LEU cc_start: 0.7690 (tp) cc_final: 0.7481 (tt) REVERT: B 987 PRO cc_start: 0.8627 (Cg_exo) cc_final: 0.8200 (Cg_endo) REVERT: B 1000 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7778 (mtt90) REVERT: B 1030 SER cc_start: 0.7816 (m) cc_final: 0.7415 (p) REVERT: B 1031 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6717 (mt-10) REVERT: B 1045 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7078 (ttpp) REVERT: B 1072 GLU cc_start: 0.6868 (pm20) cc_final: 0.6000 (mp0) REVERT: B 1123 SER cc_start: 0.7401 (t) cc_final: 0.6991 (p) REVERT: C 191 GLU cc_start: 0.7135 (tt0) cc_final: 0.6897 (tt0) REVERT: C 202 LYS cc_start: 0.6668 (tptt) cc_final: 0.6316 (mtpp) REVERT: C 279 TYR cc_start: 0.7780 (m-80) cc_final: 0.7492 (m-10) REVERT: C 365 TYR cc_start: 0.7194 (m-80) cc_final: 0.6804 (m-80) REVERT: C 537 LYS cc_start: 0.7878 (ttpt) cc_final: 0.7597 (ttmm) REVERT: C 573 THR cc_start: 0.7240 (m) cc_final: 0.6982 (p) REVERT: C 603 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8344 (t0) REVERT: C 657 ASN cc_start: 0.7417 (m-40) cc_final: 0.7107 (m-40) REVERT: C 756 TYR cc_start: 0.8218 (m-80) cc_final: 0.7644 (m-80) REVERT: C 764 ASN cc_start: 0.8182 (t0) cc_final: 0.7861 (m-40) REVERT: C 872 GLN cc_start: 0.7408 (tp40) cc_final: 0.7196 (tt0) REVERT: C 902 MET cc_start: 0.7445 (mmp) cc_final: 0.6717 (mmm) REVERT: C 984 LEU cc_start: 0.8014 (mt) cc_final: 0.7699 (mp) REVERT: C 990 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6964 (mm-30) REVERT: C 1027 THR cc_start: 0.7572 (m) cc_final: 0.7282 (m) outliers start: 87 outliers final: 46 residues processed: 511 average time/residue: 0.1527 time to fit residues: 124.8731 Evaluate side-chains 488 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 436 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 181 optimal weight: 0.7980 chunk 229 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 157 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 86 optimal weight: 0.0030 chunk 145 optimal weight: 0.8980 chunk 256 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 762 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS A1058 HIS A1083 HIS A1119 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 872 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN B1011 GLN B1048 HIS C 49 HIS C 115 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 710 ASN C 804 GLN C 969 ASN C1036 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.162779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129942 restraints weight = 36751.893| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 3.09 r_work: 0.3442 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 1.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 24284 Z= 0.238 Angle : 0.781 20.898 33126 Z= 0.398 Chirality : 0.050 0.301 3932 Planarity : 0.005 0.075 4164 Dihedral : 6.087 59.647 4422 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.11 % Allowed : 17.37 % Favored : 78.52 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 2844 helix: 0.90 (0.19), residues: 735 sheet: 0.06 (0.21), residues: 573 loop : -0.99 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C1107 TYR 0.028 0.002 TYR A 279 PHE 0.067 0.002 PHE B 58 TRP 0.013 0.002 TRP C 104 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00541 (24198) covalent geometry : angle 0.74339 (32913) SS BOND : bond 0.01292 ( 36) SS BOND : angle 2.81684 ( 72) hydrogen bonds : bond 0.05192 ( 988) hydrogen bonds : angle 5.68146 ( 2748) Misc. bond : bond 0.00250 ( 3) link_BETA1-4 : bond 0.00441 ( 15) link_BETA1-4 : angle 1.47563 ( 45) link_NAG-ASN : bond 0.00897 ( 32) link_NAG-ASN : angle 3.75616 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 568 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7300 (tp40) cc_final: 0.7046 (tp40) REVERT: A 287 ASP cc_start: 0.7076 (t70) cc_final: 0.6655 (t70) REVERT: A 298 GLU cc_start: 0.7221 (tp30) cc_final: 0.6994 (tp30) REVERT: A 305 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8218 (m) REVERT: A 306 PHE cc_start: 0.7651 (m-80) cc_final: 0.7384 (m-10) REVERT: A 329 PHE cc_start: 0.7684 (m-80) cc_final: 0.7302 (m-10) REVERT: A 531 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8304 (p) REVERT: A 663 ASP cc_start: 0.7152 (t70) cc_final: 0.6891 (t0) REVERT: A 737 ASP cc_start: 0.7241 (t0) cc_final: 0.7032 (t0) REVERT: A 754 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8690 (tt) REVERT: A 765 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7665 (ttm-80) REVERT: A 773 GLU cc_start: 0.8076 (tp30) cc_final: 0.7744 (tp30) REVERT: A 780 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7709 (tm-30) REVERT: A 790 LYS cc_start: 0.7590 (pttt) cc_final: 0.7350 (mtmm) REVERT: A 795 LYS cc_start: 0.7813 (mmtm) cc_final: 0.7611 (mmtm) REVERT: A 823 PHE cc_start: 0.7564 (m-80) cc_final: 0.7145 (m-80) REVERT: A 887 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7922 (p) REVERT: A 933 LYS cc_start: 0.7923 (mttt) cc_final: 0.7671 (mttm) REVERT: A 955 ASN cc_start: 0.8486 (m-40) cc_final: 0.8278 (m-40) REVERT: A 976 VAL cc_start: 0.8784 (t) cc_final: 0.8441 (p) REVERT: A 985 ASP cc_start: 0.7209 (p0) cc_final: 0.6966 (p0) REVERT: A 1072 GLU cc_start: 0.7664 (pp20) cc_final: 0.6992 (pt0) REVERT: B 55 PHE cc_start: 0.7491 (m-80) cc_final: 0.6684 (m-80) REVERT: B 135 PHE cc_start: 0.4774 (m-80) cc_final: 0.4485 (m-80) REVERT: B 169 GLU cc_start: 0.7342 (mp0) cc_final: 0.7003 (mp0) REVERT: B 239 GLN cc_start: 0.8175 (tt0) cc_final: 0.7552 (tm-30) REVERT: B 240 THR cc_start: 0.7915 (m) cc_final: 0.7338 (t) REVERT: B 281 GLU cc_start: 0.6029 (tp30) cc_final: 0.5713 (tp30) REVERT: B 305 SER cc_start: 0.8833 (t) cc_final: 0.8396 (p) REVERT: B 338 PHE cc_start: 0.6613 (m-80) cc_final: 0.6405 (m-80) REVERT: B 357 ARG cc_start: 0.7178 (mpt180) cc_final: 0.6122 (mpt180) REVERT: B 382 VAL cc_start: 0.8436 (t) cc_final: 0.8119 (p) REVERT: B 428 ASP cc_start: 0.6887 (t0) cc_final: 0.6530 (t0) REVERT: B 514 SER cc_start: 0.8419 (t) cc_final: 0.7864 (p) REVERT: B 515 PHE cc_start: 0.8027 (m-10) cc_final: 0.7760 (m-10) REVERT: B 644 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7425 (tp40) REVERT: B 765 ARG cc_start: 0.7987 (ttm110) cc_final: 0.7589 (ttm170) REVERT: B 774 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7884 (mp-120) REVERT: B 779 GLN cc_start: 0.7999 (tp40) cc_final: 0.7751 (tp40) REVERT: B 797 PHE cc_start: 0.7497 (m-10) cc_final: 0.7250 (m-10) REVERT: B 872 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7729 (mm-40) REVERT: B 954 GLN cc_start: 0.7577 (mt0) cc_final: 0.7130 (mt0) REVERT: B 1000 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7863 (mtt90) REVERT: B 1030 SER cc_start: 0.8549 (m) cc_final: 0.8212 (p) REVERT: B 1045 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7753 (ttpp) REVERT: C 191 GLU cc_start: 0.7372 (tt0) cc_final: 0.7170 (tt0) REVERT: C 202 LYS cc_start: 0.7344 (tptt) cc_final: 0.7088 (mtmt) REVERT: C 266 TYR cc_start: 0.7373 (m-80) cc_final: 0.7172 (m-80) REVERT: C 279 TYR cc_start: 0.7918 (m-80) cc_final: 0.7668 (m-10) REVERT: C 305 SER cc_start: 0.8968 (t) cc_final: 0.8601 (m) REVERT: C 320 VAL cc_start: 0.8469 (t) cc_final: 0.8221 (m) REVERT: C 537 LYS cc_start: 0.8064 (ttpt) cc_final: 0.7722 (ttmm) REVERT: C 554 GLU cc_start: 0.7292 (tp30) cc_final: 0.7018 (tp30) REVERT: C 614 ASP cc_start: 0.7840 (m-30) cc_final: 0.7630 (p0) REVERT: C 654 GLU cc_start: 0.8023 (tp30) cc_final: 0.7814 (tp30) REVERT: C 657 ASN cc_start: 0.7434 (m-40) cc_final: 0.7156 (m-40) REVERT: C 660 TYR cc_start: 0.8394 (m-80) cc_final: 0.8148 (m-80) REVERT: C 697 MET cc_start: 0.8079 (ttt) cc_final: 0.7835 (ttp) REVERT: C 759 PHE cc_start: 0.8214 (m-10) cc_final: 0.7886 (m-80) REVERT: C 859 THR cc_start: 0.8613 (p) cc_final: 0.8272 (t) REVERT: C 1005 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7737 (mt0) REVERT: C 1041 ASP cc_start: 0.7610 (m-30) cc_final: 0.7351 (m-30) REVERT: C 1061 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8416 (t) REVERT: C 1073 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8158 (mtpp) REVERT: C 1102 TRP cc_start: 0.8674 (m100) cc_final: 0.8321 (m100) outliers start: 105 outliers final: 55 residues processed: 632 average time/residue: 0.1590 time to fit residues: 158.3969 Evaluate side-chains 569 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 504 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1036 GLN Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 270 optimal weight: 2.9990 chunk 246 optimal weight: 0.6980 chunk 286 optimal weight: 0.3980 chunk 256 optimal weight: 0.6980 chunk 269 optimal weight: 0.5980 chunk 35 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 191 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 394 ASN ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A1119 ASN B 762 GLN B 824 ASN B 901 GLN B1048 HIS C 115 GLN C 314 GLN C 388 ASN C 784 GLN C 804 GLN C1036 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.161801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.128836 restraints weight = 36106.974| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.08 r_work: 0.3411 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 1.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 24284 Z= 0.195 Angle : 0.738 20.752 33126 Z= 0.372 Chirality : 0.048 0.308 3932 Planarity : 0.005 0.069 4164 Dihedral : 6.042 57.337 4422 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.76 % Allowed : 19.99 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 2844 helix: 1.12 (0.20), residues: 732 sheet: 0.03 (0.20), residues: 624 loop : -0.89 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 357 TYR 0.026 0.002 TYR B1138 PHE 0.020 0.002 PHE B 238 TRP 0.016 0.002 TRP C1102 HIS 0.015 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00451 (24198) covalent geometry : angle 0.68722 (32913) SS BOND : bond 0.00720 ( 36) SS BOND : angle 3.31999 ( 72) hydrogen bonds : bond 0.04746 ( 988) hydrogen bonds : angle 5.61333 ( 2748) Misc. bond : bond 0.00114 ( 3) link_BETA1-4 : bond 0.00369 ( 15) link_BETA1-4 : angle 1.32089 ( 45) link_NAG-ASN : bond 0.00796 ( 32) link_NAG-ASN : angle 4.09130 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 541 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7356 (tp40) cc_final: 0.7080 (tp40) REVERT: A 54 LEU cc_start: 0.8453 (mt) cc_final: 0.8136 (mp) REVERT: A 240 THR cc_start: 0.7649 (m) cc_final: 0.7448 (m) REVERT: A 287 ASP cc_start: 0.7229 (t70) cc_final: 0.6849 (t70) REVERT: A 298 GLU cc_start: 0.7187 (tp30) cc_final: 0.6932 (tp30) REVERT: A 306 PHE cc_start: 0.7887 (m-80) cc_final: 0.7554 (m-80) REVERT: A 329 PHE cc_start: 0.7651 (m-80) cc_final: 0.7385 (m-10) REVERT: A 428 ASP cc_start: 0.7352 (p0) cc_final: 0.6990 (p0) REVERT: A 429 PHE cc_start: 0.7600 (t80) cc_final: 0.7262 (t80) REVERT: A 531 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8385 (p) REVERT: A 663 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6980 (t0) REVERT: A 702 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7663 (tm-30) REVERT: A 754 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8678 (tt) REVERT: A 765 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7613 (ttm-80) REVERT: A 773 GLU cc_start: 0.7946 (tp30) cc_final: 0.7745 (tp30) REVERT: A 790 LYS cc_start: 0.7709 (pttt) cc_final: 0.7432 (mtmm) REVERT: A 795 LYS cc_start: 0.7903 (mmtm) cc_final: 0.7631 (mmtm) REVERT: A 823 PHE cc_start: 0.7672 (m-80) cc_final: 0.7267 (m-80) REVERT: A 872 GLN cc_start: 0.8284 (tp-100) cc_final: 0.8024 (tp40) REVERT: A 887 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7903 (p) REVERT: A 933 LYS cc_start: 0.7917 (mttt) cc_final: 0.7565 (mtmm) REVERT: A 1010 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7859 (mp10) REVERT: A 1012 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8263 (mt) REVERT: A 1072 GLU cc_start: 0.7526 (pp20) cc_final: 0.6848 (tm-30) REVERT: A 1118 ASP cc_start: 0.7342 (t0) cc_final: 0.6984 (t0) REVERT: B 55 PHE cc_start: 0.7471 (m-80) cc_final: 0.6778 (m-80) REVERT: B 135 PHE cc_start: 0.4910 (m-80) cc_final: 0.4589 (m-80) REVERT: B 169 GLU cc_start: 0.7353 (mp0) cc_final: 0.6940 (mp0) REVERT: B 206 LYS cc_start: 0.7962 (tptt) cc_final: 0.7685 (tptt) REVERT: B 237 ARG cc_start: 0.7036 (mtp85) cc_final: 0.6726 (mtp85) REVERT: B 239 GLN cc_start: 0.8142 (tt0) cc_final: 0.7767 (tt0) REVERT: B 240 THR cc_start: 0.7940 (m) cc_final: 0.7739 (t) REVERT: B 281 GLU cc_start: 0.6205 (tp30) cc_final: 0.5846 (tp30) REVERT: B 357 ARG cc_start: 0.7114 (mpt180) cc_final: 0.5674 (mpt180) REVERT: B 382 VAL cc_start: 0.8564 (t) cc_final: 0.8133 (p) REVERT: B 396 TYR cc_start: 0.7585 (m-80) cc_final: 0.6606 (m-80) REVERT: B 428 ASP cc_start: 0.7009 (t0) cc_final: 0.6712 (t0) REVERT: B 514 SER cc_start: 0.8505 (t) cc_final: 0.7905 (p) REVERT: B 515 PHE cc_start: 0.8152 (m-10) cc_final: 0.7838 (m-10) REVERT: B 549 THR cc_start: 0.8229 (t) cc_final: 0.7691 (p) REVERT: B 644 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7474 (tp40) REVERT: B 707 TYR cc_start: 0.8359 (t80) cc_final: 0.7812 (t80) REVERT: B 726 ILE cc_start: 0.8506 (mm) cc_final: 0.8254 (mm) REVERT: B 765 ARG cc_start: 0.8037 (ttm110) cc_final: 0.7602 (ttm170) REVERT: B 774 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7815 (mp-120) REVERT: B 790 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7960 (ttmm) REVERT: B 815 ARG cc_start: 0.7312 (ptp-170) cc_final: 0.7046 (ptt180) REVERT: B 824 ASN cc_start: 0.6906 (OUTLIER) cc_final: 0.6705 (t160) REVERT: B 933 LYS cc_start: 0.7774 (mttt) cc_final: 0.7455 (mmtm) REVERT: B 954 GLN cc_start: 0.7685 (mt0) cc_final: 0.7462 (mt0) REVERT: B 1000 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8115 (mtt90) REVERT: B 1002 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7371 (tm-30) REVERT: B 1030 SER cc_start: 0.8638 (m) cc_final: 0.8247 (p) REVERT: B 1045 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7990 (tttm) REVERT: B 1050 MET cc_start: 0.8562 (mtp) cc_final: 0.8351 (mtm) REVERT: B 1084 ASP cc_start: 0.7748 (m-30) cc_final: 0.7260 (m-30) REVERT: C 32 PHE cc_start: 0.7159 (t80) cc_final: 0.6848 (m-80) REVERT: C 191 GLU cc_start: 0.7265 (tt0) cc_final: 0.6714 (tt0) REVERT: C 202 LYS cc_start: 0.7507 (tptt) cc_final: 0.7277 (mtmt) REVERT: C 240 THR cc_start: 0.8362 (m) cc_final: 0.7842 (t) REVERT: C 266 TYR cc_start: 0.7441 (m-80) cc_final: 0.7172 (m-80) REVERT: C 305 SER cc_start: 0.8957 (t) cc_final: 0.8604 (m) REVERT: C 320 VAL cc_start: 0.8625 (t) cc_final: 0.8371 (m) REVERT: C 573 THR cc_start: 0.7786 (m) cc_final: 0.7485 (p) REVERT: C 583 GLU cc_start: 0.7616 (pm20) cc_final: 0.7338 (pm20) REVERT: C 654 GLU cc_start: 0.8126 (tp30) cc_final: 0.7874 (tp30) REVERT: C 657 ASN cc_start: 0.7439 (m-40) cc_final: 0.7130 (m-40) REVERT: C 660 TYR cc_start: 0.8441 (m-80) cc_final: 0.8234 (m-80) REVERT: C 731 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7954 (pmm) REVERT: C 736 VAL cc_start: 0.8380 (m) cc_final: 0.8126 (t) REVERT: C 759 PHE cc_start: 0.8087 (m-10) cc_final: 0.7841 (m-80) REVERT: C 779 GLN cc_start: 0.8548 (tp40) cc_final: 0.8149 (tm-30) REVERT: C 931 ILE cc_start: 0.7268 (mm) cc_final: 0.7041 (mm) REVERT: C 988 GLU cc_start: 0.7802 (pm20) cc_final: 0.7585 (mp0) REVERT: C 1005 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7636 (mt0) REVERT: C 1036 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7725 (mt0) REVERT: C 1041 ASP cc_start: 0.7638 (m-30) cc_final: 0.7367 (m-30) REVERT: C 1073 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8179 (mtpp) REVERT: C 1102 TRP cc_start: 0.8351 (m100) cc_final: 0.8127 (m100) REVERT: C 1133 VAL cc_start: 0.8689 (p) cc_final: 0.8258 (m) outliers start: 96 outliers final: 47 residues processed: 598 average time/residue: 0.1667 time to fit residues: 155.3862 Evaluate side-chains 563 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 502 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1036 GLN Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 47 optimal weight: 3.9990 chunk 247 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.0010 chunk 91 optimal weight: 0.5980 chunk 130 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 762 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 949 GLN B 955 ASN B1048 HIS B1119 ASN C 314 GLN C1125 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.162667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.129553 restraints weight = 35992.847| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.09 r_work: 0.3415 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 1.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 24284 Z= 0.148 Angle : 0.697 20.784 33126 Z= 0.354 Chirality : 0.046 0.308 3932 Planarity : 0.004 0.062 4164 Dihedral : 5.783 55.938 4422 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.25 % Allowed : 21.56 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.15), residues: 2844 helix: 1.33 (0.20), residues: 732 sheet: -0.01 (0.20), residues: 654 loop : -0.83 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 357 TYR 0.024 0.001 TYR A1067 PHE 0.020 0.002 PHE C 201 TRP 0.009 0.001 TRP C1102 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00346 (24198) covalent geometry : angle 0.64960 (32913) SS BOND : bond 0.00656 ( 36) SS BOND : angle 3.32260 ( 72) hydrogen bonds : bond 0.04225 ( 988) hydrogen bonds : angle 5.46625 ( 2748) Misc. bond : bond 0.00111 ( 3) link_BETA1-4 : bond 0.00380 ( 15) link_BETA1-4 : angle 1.25877 ( 45) link_NAG-ASN : bond 0.00721 ( 32) link_NAG-ASN : angle 3.75683 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 525 time to evaluate : 0.761 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 52 GLN cc_start: 0.7410 (tp40) cc_final: 0.7100 (tp40) REVERT: A 240 THR cc_start: 0.7629 (m) cc_final: 0.7427 (m) REVERT: A 306 PHE cc_start: 0.7919 (m-80) cc_final: 0.7676 (m-80) REVERT: A 329 PHE cc_start: 0.7698 (m-80) cc_final: 0.7446 (m-10) REVERT: A 428 ASP cc_start: 0.7342 (p0) cc_final: 0.7070 (p0) REVERT: A 429 PHE cc_start: 0.7712 (t80) cc_final: 0.7357 (t80) REVERT: A 531 THR cc_start: 0.8681 (t) cc_final: 0.8415 (p) REVERT: A 537 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8198 (mtpp) REVERT: A 663 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.6982 (t0) REVERT: A 765 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7560 (ttm-80) REVERT: A 790 LYS cc_start: 0.7732 (pttt) cc_final: 0.6696 (mtmm) REVERT: A 795 LYS cc_start: 0.7901 (mmtm) cc_final: 0.7619 (mmtm) REVERT: A 872 GLN cc_start: 0.8269 (tp-100) cc_final: 0.7925 (tt0) REVERT: A 933 LYS cc_start: 0.8059 (mttt) cc_final: 0.7667 (mtmm) REVERT: A 949 GLN cc_start: 0.7035 (tp40) cc_final: 0.6711 (tp40) REVERT: A 1010 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7809 (mp10) REVERT: A 1012 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8249 (mt) REVERT: A 1072 GLU cc_start: 0.7444 (pp20) cc_final: 0.6813 (tm-30) REVERT: A 1135 ASN cc_start: 0.7374 (t0) cc_final: 0.7140 (m-40) REVERT: B 55 PHE cc_start: 0.7447 (m-80) cc_final: 0.6806 (m-80) REVERT: B 135 PHE cc_start: 0.4926 (m-80) cc_final: 0.4623 (m-80) REVERT: B 206 LYS cc_start: 0.7915 (tptt) cc_final: 0.7623 (tptt) REVERT: B 237 ARG cc_start: 0.7026 (mtp85) cc_final: 0.6682 (mtp85) REVERT: B 281 GLU cc_start: 0.6295 (tp30) cc_final: 0.5900 (tp30) REVERT: B 357 ARG cc_start: 0.7087 (mpt180) cc_final: 0.6595 (mpt180) REVERT: B 365 TYR cc_start: 0.7841 (m-80) cc_final: 0.7345 (m-80) REVERT: B 428 ASP cc_start: 0.7063 (t0) cc_final: 0.6791 (t0) REVERT: B 514 SER cc_start: 0.8463 (t) cc_final: 0.7867 (p) REVERT: B 515 PHE cc_start: 0.8168 (m-10) cc_final: 0.7935 (m-10) REVERT: B 549 THR cc_start: 0.8264 (t) cc_final: 0.7769 (p) REVERT: B 554 GLU cc_start: 0.7522 (pm20) cc_final: 0.7166 (pm20) REVERT: B 567 ARG cc_start: 0.7686 (tpp80) cc_final: 0.7417 (tpp80) REVERT: B 597 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8304 (m) REVERT: B 644 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7493 (tp40) REVERT: B 651 ILE cc_start: 0.8517 (mt) cc_final: 0.8263 (mt) REVERT: B 716 THR cc_start: 0.8807 (t) cc_final: 0.8590 (p) REVERT: B 726 ILE cc_start: 0.8487 (mm) cc_final: 0.8103 (mm) REVERT: B 765 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7510 (ttm170) REVERT: B 774 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7880 (mp-120) REVERT: B 790 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8022 (mtpp) REVERT: B 797 PHE cc_start: 0.7626 (m-10) cc_final: 0.7369 (m-10) REVERT: B 815 ARG cc_start: 0.7541 (ptp-170) cc_final: 0.7247 (ptt180) REVERT: B 823 PHE cc_start: 0.7381 (m-80) cc_final: 0.6855 (m-80) REVERT: B 960 ASN cc_start: 0.8498 (m-40) cc_final: 0.8191 (t0) REVERT: B 1000 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8042 (mtt90) REVERT: B 1045 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7939 (mtpp) REVERT: B 1084 ASP cc_start: 0.7780 (m-30) cc_final: 0.7297 (m-30) REVERT: B 1135 ASN cc_start: 0.8064 (t0) cc_final: 0.7626 (t0) REVERT: C 32 PHE cc_start: 0.7186 (t80) cc_final: 0.6909 (m-80) REVERT: C 113 LYS cc_start: 0.7027 (tptp) cc_final: 0.6760 (tptp) REVERT: C 191 GLU cc_start: 0.7186 (tt0) cc_final: 0.6642 (tt0) REVERT: C 195 LYS cc_start: 0.8245 (ptmt) cc_final: 0.7984 (ptmt) REVERT: C 202 LYS cc_start: 0.7486 (tptt) cc_final: 0.7254 (mtmt) REVERT: C 203 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7747 (mt) REVERT: C 240 THR cc_start: 0.8305 (m) cc_final: 0.7819 (t) REVERT: C 266 TYR cc_start: 0.7467 (m-80) cc_final: 0.7165 (m-80) REVERT: C 305 SER cc_start: 0.8959 (t) cc_final: 0.8655 (m) REVERT: C 320 VAL cc_start: 0.8618 (t) cc_final: 0.8311 (m) REVERT: C 355 ARG cc_start: 0.8085 (mmm160) cc_final: 0.7878 (mmm160) REVERT: C 357 ARG cc_start: 0.6782 (ttt-90) cc_final: 0.6262 (ttt-90) REVERT: C 516 GLU cc_start: 0.6847 (tm-30) cc_final: 0.6581 (tm-30) REVERT: C 551 VAL cc_start: 0.8791 (m) cc_final: 0.8557 (p) REVERT: C 573 THR cc_start: 0.7818 (m) cc_final: 0.7565 (p) REVERT: C 583 GLU cc_start: 0.7639 (pm20) cc_final: 0.7227 (mp0) REVERT: C 654 GLU cc_start: 0.8114 (tp30) cc_final: 0.7896 (tp30) REVERT: C 657 ASN cc_start: 0.7444 (m-40) cc_final: 0.7120 (m-40) REVERT: C 660 TYR cc_start: 0.8427 (m-80) cc_final: 0.8190 (m-80) REVERT: C 731 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7998 (pmm) REVERT: C 745 ASP cc_start: 0.7766 (t0) cc_final: 0.7384 (t0) REVERT: C 762 GLN cc_start: 0.7928 (mm110) cc_final: 0.7694 (mm-40) REVERT: C 773 GLU cc_start: 0.7749 (tp30) cc_final: 0.7086 (tm-30) REVERT: C 775 ASP cc_start: 0.7814 (t70) cc_final: 0.7588 (t0) REVERT: C 779 GLN cc_start: 0.8508 (tp40) cc_final: 0.8121 (tm-30) REVERT: C 931 ILE cc_start: 0.7396 (mm) cc_final: 0.7106 (mm) REVERT: C 988 GLU cc_start: 0.7799 (pm20) cc_final: 0.7558 (mp0) REVERT: C 1005 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7668 (mt0) REVERT: C 1041 ASP cc_start: 0.7648 (m-30) cc_final: 0.7368 (m-30) REVERT: C 1133 VAL cc_start: 0.8663 (p) cc_final: 0.8306 (m) outliers start: 83 outliers final: 51 residues processed: 575 average time/residue: 0.1642 time to fit residues: 147.6135 Evaluate side-chains 564 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 503 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 121 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 276 optimal weight: 0.9980 chunk 112 optimal weight: 0.0040 chunk 174 optimal weight: 1.9990 chunk 21 optimal weight: 0.0050 chunk 281 optimal weight: 0.9990 chunk 242 optimal weight: 0.4980 chunk 115 optimal weight: 0.9990 overall best weight: 0.3206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B 955 ASN B1048 HIS B1119 ASN C 314 GLN C1036 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.162149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.128838 restraints weight = 36330.106| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.12 r_work: 0.3411 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 1.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24284 Z= 0.144 Angle : 0.693 20.069 33126 Z= 0.351 Chirality : 0.046 0.449 3932 Planarity : 0.004 0.062 4164 Dihedral : 5.566 55.092 4422 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.93 % Allowed : 22.14 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.15), residues: 2844 helix: 1.49 (0.20), residues: 732 sheet: 0.01 (0.19), residues: 690 loop : -0.78 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 577 TYR 0.023 0.001 TYR A1067 PHE 0.021 0.001 PHE B 797 TRP 0.008 0.001 TRP C1102 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00338 (24198) covalent geometry : angle 0.64879 (32913) SS BOND : bond 0.00718 ( 36) SS BOND : angle 3.34598 ( 72) hydrogen bonds : bond 0.04043 ( 988) hydrogen bonds : angle 5.37529 ( 2748) Misc. bond : bond 0.00101 ( 3) link_BETA1-4 : bond 0.00399 ( 15) link_BETA1-4 : angle 1.23499 ( 45) link_NAG-ASN : bond 0.00718 ( 32) link_NAG-ASN : angle 3.49826 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 514 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7453 (tp40) cc_final: 0.7146 (tp40) REVERT: A 106 PHE cc_start: 0.7464 (m-80) cc_final: 0.7044 (m-80) REVERT: A 240 THR cc_start: 0.7690 (m) cc_final: 0.7483 (m) REVERT: A 309 GLU cc_start: 0.7171 (tm-30) cc_final: 0.6871 (tp30) REVERT: A 329 PHE cc_start: 0.7598 (m-80) cc_final: 0.7180 (m-10) REVERT: A 378 LYS cc_start: 0.7637 (mttt) cc_final: 0.7034 (mtpt) REVERT: A 406 GLU cc_start: 0.7421 (pm20) cc_final: 0.6963 (pm20) REVERT: A 428 ASP cc_start: 0.7404 (p0) cc_final: 0.7031 (p0) REVERT: A 429 PHE cc_start: 0.7817 (t80) cc_final: 0.7436 (t80) REVERT: A 531 THR cc_start: 0.8665 (t) cc_final: 0.8432 (p) REVERT: A 537 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8227 (mtpp) REVERT: A 663 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7111 (t0) REVERT: A 754 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8644 (tt) REVERT: A 765 ARG cc_start: 0.7808 (mtp85) cc_final: 0.7567 (ttm-80) REVERT: A 779 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7751 (tm-30) REVERT: A 795 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7631 (mmtm) REVERT: A 872 GLN cc_start: 0.8261 (tp-100) cc_final: 0.7957 (tt0) REVERT: A 933 LYS cc_start: 0.8074 (mttt) cc_final: 0.7660 (mtmm) REVERT: A 949 GLN cc_start: 0.7075 (tp40) cc_final: 0.6760 (tp40) REVERT: A 1010 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7837 (mp10) REVERT: A 1050 MET cc_start: 0.8334 (ptp) cc_final: 0.8095 (ptp) REVERT: A 1135 ASN cc_start: 0.7534 (t0) cc_final: 0.7307 (m-40) REVERT: B 55 PHE cc_start: 0.7448 (m-80) cc_final: 0.6903 (m-80) REVERT: B 206 LYS cc_start: 0.7978 (tptt) cc_final: 0.7701 (tptt) REVERT: B 237 ARG cc_start: 0.7059 (mtp85) cc_final: 0.6717 (mtp85) REVERT: B 239 GLN cc_start: 0.8047 (tt0) cc_final: 0.7360 (tm-30) REVERT: B 281 GLU cc_start: 0.6355 (tp30) cc_final: 0.5926 (tp30) REVERT: B 306 PHE cc_start: 0.8233 (t80) cc_final: 0.7655 (t80) REVERT: B 357 ARG cc_start: 0.7091 (mpt180) cc_final: 0.6573 (mpt180) REVERT: B 365 TYR cc_start: 0.7885 (m-80) cc_final: 0.7198 (m-80) REVERT: B 428 ASP cc_start: 0.7060 (t0) cc_final: 0.6799 (p0) REVERT: B 514 SER cc_start: 0.8450 (t) cc_final: 0.7861 (p) REVERT: B 515 PHE cc_start: 0.8213 (m-10) cc_final: 0.8012 (m-10) REVERT: B 549 THR cc_start: 0.8291 (t) cc_final: 0.7819 (p) REVERT: B 554 GLU cc_start: 0.7477 (pm20) cc_final: 0.7111 (pm20) REVERT: B 567 ARG cc_start: 0.7680 (tpp80) cc_final: 0.7214 (ttm-80) REVERT: B 597 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8295 (m) REVERT: B 644 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7562 (tp40) REVERT: B 651 ILE cc_start: 0.8592 (mt) cc_final: 0.8327 (mt) REVERT: B 726 ILE cc_start: 0.8491 (mm) cc_final: 0.8115 (mm) REVERT: B 765 ARG cc_start: 0.7925 (ttm110) cc_final: 0.7538 (ttm170) REVERT: B 774 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7841 (mp-120) REVERT: B 790 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8045 (mtpp) REVERT: B 797 PHE cc_start: 0.7630 (m-10) cc_final: 0.7400 (m-10) REVERT: B 815 ARG cc_start: 0.7679 (ptp-170) cc_final: 0.7402 (ptt180) REVERT: B 960 ASN cc_start: 0.8516 (m-40) cc_final: 0.8219 (t0) REVERT: B 977 LEU cc_start: 0.8125 (mm) cc_final: 0.7795 (mt) REVERT: B 979 ASP cc_start: 0.8144 (m-30) cc_final: 0.7657 (t0) REVERT: B 987 PRO cc_start: 0.8698 (Cg_exo) cc_final: 0.8474 (Cg_endo) REVERT: B 1000 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8060 (mtt90) REVERT: B 1045 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7994 (mtpp) REVERT: B 1135 ASN cc_start: 0.8230 (t0) cc_final: 0.7978 (t0) REVERT: C 32 PHE cc_start: 0.7198 (t80) cc_final: 0.6909 (m-10) REVERT: C 191 GLU cc_start: 0.7261 (tt0) cc_final: 0.6658 (tt0) REVERT: C 202 LYS cc_start: 0.7499 (tptt) cc_final: 0.7249 (mtmt) REVERT: C 203 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7758 (mt) REVERT: C 240 THR cc_start: 0.8303 (m) cc_final: 0.7813 (t) REVERT: C 305 SER cc_start: 0.8978 (t) cc_final: 0.8683 (m) REVERT: C 320 VAL cc_start: 0.8644 (t) cc_final: 0.8329 (m) REVERT: C 551 VAL cc_start: 0.8727 (m) cc_final: 0.8495 (p) REVERT: C 573 THR cc_start: 0.7855 (m) cc_final: 0.7608 (p) REVERT: C 583 GLU cc_start: 0.7727 (pm20) cc_final: 0.7401 (pm20) REVERT: C 654 GLU cc_start: 0.8093 (tp30) cc_final: 0.7838 (tp30) REVERT: C 657 ASN cc_start: 0.7498 (m-40) cc_final: 0.7195 (m-40) REVERT: C 660 TYR cc_start: 0.8428 (m-80) cc_final: 0.8204 (m-80) REVERT: C 731 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7885 (pmm) REVERT: C 736 VAL cc_start: 0.8410 (m) cc_final: 0.8159 (t) REVERT: C 745 ASP cc_start: 0.7757 (t0) cc_final: 0.7397 (t0) REVERT: C 759 PHE cc_start: 0.8032 (m-80) cc_final: 0.7799 (m-80) REVERT: C 775 ASP cc_start: 0.7857 (t70) cc_final: 0.7645 (t0) REVERT: C 779 GLN cc_start: 0.8448 (tp40) cc_final: 0.8034 (tm-30) REVERT: C 931 ILE cc_start: 0.7506 (mm) cc_final: 0.7237 (mm) REVERT: C 988 GLU cc_start: 0.7915 (pm20) cc_final: 0.7644 (mp0) REVERT: C 1041 ASP cc_start: 0.7725 (m-30) cc_final: 0.7422 (m-30) REVERT: C 1133 VAL cc_start: 0.8676 (p) cc_final: 0.8332 (m) outliers start: 75 outliers final: 46 residues processed: 560 average time/residue: 0.1586 time to fit residues: 138.9592 Evaluate side-chains 575 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 519 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 83 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 20 optimal weight: 0.0000 chunk 208 optimal weight: 0.0270 chunk 241 optimal weight: 2.9990 chunk 135 optimal weight: 30.0000 chunk 184 optimal weight: 0.8980 chunk 187 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 10 optimal weight: 0.0050 chunk 82 optimal weight: 0.6980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS B1119 ASN C 314 GLN C 955 ASN C1005 GLN C1010 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.162831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.129664 restraints weight = 36180.673| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.11 r_work: 0.3420 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 1.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24284 Z= 0.136 Angle : 0.681 19.422 33126 Z= 0.347 Chirality : 0.046 0.437 3932 Planarity : 0.004 0.061 4164 Dihedral : 5.375 54.576 4422 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.39 % Allowed : 23.08 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2844 helix: 1.46 (0.20), residues: 750 sheet: 0.03 (0.19), residues: 690 loop : -0.73 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 355 TYR 0.023 0.001 TYR A1067 PHE 0.022 0.001 PHE C 201 TRP 0.009 0.001 TRP C1102 HIS 0.010 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00317 (24198) covalent geometry : angle 0.64068 (32913) SS BOND : bond 0.00608 ( 36) SS BOND : angle 3.02570 ( 72) hydrogen bonds : bond 0.03929 ( 988) hydrogen bonds : angle 5.32645 ( 2748) Misc. bond : bond 0.00094 ( 3) link_BETA1-4 : bond 0.00352 ( 15) link_BETA1-4 : angle 1.19759 ( 45) link_NAG-ASN : bond 0.00733 ( 32) link_NAG-ASN : angle 3.41210 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 538 time to evaluate : 0.670 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 52 GLN cc_start: 0.7390 (tp40) cc_final: 0.7102 (tp40) REVERT: A 106 PHE cc_start: 0.7445 (m-80) cc_final: 0.7018 (m-80) REVERT: A 309 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6865 (tp30) REVERT: A 329 PHE cc_start: 0.7604 (m-80) cc_final: 0.7307 (m-10) REVERT: A 428 ASP cc_start: 0.7412 (p0) cc_final: 0.7131 (p0) REVERT: A 429 PHE cc_start: 0.7830 (t80) cc_final: 0.7419 (t80) REVERT: A 531 THR cc_start: 0.8673 (t) cc_final: 0.8462 (p) REVERT: A 537 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8187 (mtpp) REVERT: A 663 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6889 (t0) REVERT: A 773 GLU cc_start: 0.7983 (tp30) cc_final: 0.7331 (tp30) REVERT: A 779 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7723 (tm-30) REVERT: A 795 LYS cc_start: 0.7894 (mmtm) cc_final: 0.7377 (mmtm) REVERT: A 872 GLN cc_start: 0.8240 (tp-100) cc_final: 0.7982 (tt0) REVERT: A 918 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7687 (mm-30) REVERT: A 931 ILE cc_start: 0.7940 (mm) cc_final: 0.7679 (mm) REVERT: A 933 LYS cc_start: 0.8117 (mttt) cc_final: 0.7683 (mtmm) REVERT: A 949 GLN cc_start: 0.7114 (tp40) cc_final: 0.6816 (tp40) REVERT: A 957 GLN cc_start: 0.7909 (mm110) cc_final: 0.7647 (mm110) REVERT: A 983 ARG cc_start: 0.8619 (mtp180) cc_final: 0.8318 (mtm180) REVERT: A 987 PRO cc_start: 0.8854 (Cg_exo) cc_final: 0.8640 (Cg_endo) REVERT: A 995 ARG cc_start: 0.8192 (tpp80) cc_final: 0.7847 (mtt-85) REVERT: A 1005 GLN cc_start: 0.8218 (tp40) cc_final: 0.7969 (tt0) REVERT: A 1010 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7844 (mp10) REVERT: A 1014 ARG cc_start: 0.8267 (tpp80) cc_final: 0.7948 (ttm170) REVERT: A 1050 MET cc_start: 0.8325 (ptp) cc_final: 0.8108 (ptp) REVERT: A 1135 ASN cc_start: 0.7545 (t0) cc_final: 0.7327 (m-40) REVERT: B 55 PHE cc_start: 0.7461 (m-80) cc_final: 0.6932 (m-80) REVERT: B 206 LYS cc_start: 0.7983 (tptt) cc_final: 0.7698 (tptt) REVERT: B 237 ARG cc_start: 0.7033 (mtp85) cc_final: 0.6757 (mtp85) REVERT: B 239 GLN cc_start: 0.7974 (tt0) cc_final: 0.7305 (tm-30) REVERT: B 281 GLU cc_start: 0.6479 (tp30) cc_final: 0.6048 (tp30) REVERT: B 306 PHE cc_start: 0.8117 (t80) cc_final: 0.7587 (t80) REVERT: B 357 ARG cc_start: 0.7118 (mpt180) cc_final: 0.6603 (mpt180) REVERT: B 365 TYR cc_start: 0.7910 (m-80) cc_final: 0.7276 (m-80) REVERT: B 398 ASP cc_start: 0.7935 (m-30) cc_final: 0.7724 (m-30) REVERT: B 428 ASP cc_start: 0.7098 (t0) cc_final: 0.6837 (t0) REVERT: B 514 SER cc_start: 0.8408 (t) cc_final: 0.7809 (p) REVERT: B 515 PHE cc_start: 0.8210 (m-10) cc_final: 0.8004 (m-10) REVERT: B 549 THR cc_start: 0.8277 (t) cc_final: 0.7836 (p) REVERT: B 554 GLU cc_start: 0.7450 (pm20) cc_final: 0.7125 (pm20) REVERT: B 597 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8234 (m) REVERT: B 651 ILE cc_start: 0.8575 (mt) cc_final: 0.8307 (mt) REVERT: B 765 ARG cc_start: 0.7878 (ttm110) cc_final: 0.7480 (ttm170) REVERT: B 774 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7829 (mp-120) REVERT: B 790 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7928 (mtpp) REVERT: B 815 ARG cc_start: 0.7746 (ptp-170) cc_final: 0.7483 (ptt180) REVERT: B 823 PHE cc_start: 0.7645 (m-80) cc_final: 0.7184 (m-80) REVERT: B 872 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7896 (mm-40) REVERT: B 934 ILE cc_start: 0.7955 (mm) cc_final: 0.7630 (tt) REVERT: B 954 GLN cc_start: 0.7175 (mt0) cc_final: 0.6659 (mt0) REVERT: B 960 ASN cc_start: 0.8473 (m-40) cc_final: 0.8194 (t0) REVERT: B 977 LEU cc_start: 0.8146 (mm) cc_final: 0.7822 (mt) REVERT: B 987 PRO cc_start: 0.8654 (Cg_exo) cc_final: 0.8415 (Cg_endo) REVERT: B 1000 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7969 (mtt90) REVERT: B 1045 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7940 (mtpp) REVERT: B 1063 LEU cc_start: 0.8261 (tp) cc_final: 0.8004 (mp) REVERT: C 32 PHE cc_start: 0.7245 (t80) cc_final: 0.6901 (m-10) REVERT: C 202 LYS cc_start: 0.7486 (tptt) cc_final: 0.7260 (mtmt) REVERT: C 203 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7792 (mt) REVERT: C 240 THR cc_start: 0.8305 (m) cc_final: 0.7830 (t) REVERT: C 305 SER cc_start: 0.8973 (t) cc_final: 0.8688 (m) REVERT: C 320 VAL cc_start: 0.8589 (t) cc_final: 0.8257 (m) REVERT: C 529 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7769 (mmtt) REVERT: C 551 VAL cc_start: 0.8731 (m) cc_final: 0.8528 (p) REVERT: C 573 THR cc_start: 0.7883 (m) cc_final: 0.7592 (p) REVERT: C 654 GLU cc_start: 0.8101 (tp30) cc_final: 0.7840 (tp30) REVERT: C 657 ASN cc_start: 0.7531 (m-40) cc_final: 0.7229 (m-40) REVERT: C 731 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7791 (pmm) REVERT: C 734 THR cc_start: 0.8288 (m) cc_final: 0.8023 (p) REVERT: C 736 VAL cc_start: 0.8422 (m) cc_final: 0.8148 (t) REVERT: C 745 ASP cc_start: 0.7759 (t0) cc_final: 0.7439 (t0) REVERT: C 773 GLU cc_start: 0.7564 (tp30) cc_final: 0.7275 (tp30) REVERT: C 775 ASP cc_start: 0.7822 (t70) cc_final: 0.7613 (t0) REVERT: C 779 GLN cc_start: 0.8422 (tp40) cc_final: 0.7962 (tm-30) REVERT: C 869 MET cc_start: 0.8514 (mtp) cc_final: 0.8232 (mtm) REVERT: C 931 ILE cc_start: 0.7559 (mm) cc_final: 0.7344 (mm) REVERT: C 988 GLU cc_start: 0.7935 (pm20) cc_final: 0.7681 (mp0) REVERT: C 1041 ASP cc_start: 0.7815 (m-30) cc_final: 0.7510 (m-30) REVERT: C 1133 VAL cc_start: 0.8697 (p) cc_final: 0.8379 (m) outliers start: 61 outliers final: 46 residues processed: 574 average time/residue: 0.1646 time to fit residues: 146.1434 Evaluate side-chains 564 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 509 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 48 optimal weight: 0.9980 chunk 273 optimal weight: 0.9980 chunk 226 optimal weight: 0.1980 chunk 251 optimal weight: 0.2980 chunk 88 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 265 optimal weight: 0.3980 chunk 121 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 655 HIS ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1048 HIS C 314 GLN C 710 ASN C 762 GLN C1010 GLN C1048 HIS ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.160557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.127446 restraints weight = 35923.063| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.06 r_work: 0.3386 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 1.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24284 Z= 0.166 Angle : 0.708 19.542 33126 Z= 0.358 Chirality : 0.047 0.395 3932 Planarity : 0.005 0.068 4164 Dihedral : 5.435 56.335 4422 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.86 % Allowed : 22.97 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 2844 helix: 1.37 (0.20), residues: 753 sheet: 0.01 (0.19), residues: 672 loop : -0.77 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1000 TYR 0.027 0.001 TYR A1067 PHE 0.025 0.002 PHE A 201 TRP 0.010 0.001 TRP B1102 HIS 0.009 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00391 (24198) covalent geometry : angle 0.66957 (32913) SS BOND : bond 0.00758 ( 36) SS BOND : angle 3.06118 ( 72) hydrogen bonds : bond 0.04225 ( 988) hydrogen bonds : angle 5.35380 ( 2748) Misc. bond : bond 0.00084 ( 3) link_BETA1-4 : bond 0.00386 ( 15) link_BETA1-4 : angle 1.26441 ( 45) link_NAG-ASN : bond 0.00726 ( 32) link_NAG-ASN : angle 3.38243 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5264.97 seconds wall clock time: 91 minutes 12.98 seconds (5472.98 seconds total)