Starting phenix.real_space_refine on Sat Jul 4 22:16:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q1z_13776/07_2026/7q1z_13776.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q1z_13776/07_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_13776/07_2026/7q1z_13776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q1z_13776/07_2026/7q1z_13776.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7q1z_13776/07_2026/7q1z_13776.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q1z_13776/07_2026/7q1z_13776.cif" model { file = "/net/cci-nas-00/data/ceres_data/7q1z_13776/07_2026/7q1z_13776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q1z_13776/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 11 Time building chain proxies: 5.46, per 1000 atoms: 0.23 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: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.10 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: 5.90 Time building geometry restraints manager: 2.90 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: 12989 17.91 - 35.82: 701 35.82 - 53.73: 135 53.73 - 71.64: 53 71.64 - 89.55: 27 Dihedral angle restraints: 13905 sinusoidal: 5415 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 13902 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: 0.03 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: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.200 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3117 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 : 12.709 89.552 8313 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/Z covalent geometry : bond 0.00419 / 0.20 (24198) covalent geometry : angle 0.60657 / 0.34 (32913) SS BOND : bond 0.00455 / 0.30 ( 36) SS BOND : angle 1.17292 / 0.72 ( 72) hydrogen bonds : bond 0.17339 / 11.27 ( 988) hydrogen bonds : angle 7.63170 / 5.48 ( 2748) Misc. bond : bond 0.00024 / 0.01 ( 3) link_BETA1-4 : bond 0.00314 / 0.18 ( 15) link_BETA1-4 : angle 1.25037 / 0.81 ( 45) link_NAG-ASN : bond 0.00260 / 0.14 ( 32) link_NAG-ASN : angle 1.87734 / 1.34 ( 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 : 0.748 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: 0.1665 time to fit residues: 88.6501 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 : 0.759 ------------------------------------------------------------------------------- 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... A 409 GLN A 556 ASN A 655 HIS A 675 GLN A 764 ASN A 955 ASN B 134 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.167545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.137477 restraints weight = 37163.283| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.95 r_work: 0.3535 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5019 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 24284 Z= 0.296 Angle : 0.976 25.194 33126 Z= 0.481 Chirality : 0.064 1.865 3932 Planarity : 0.007 0.093 4164 Dihedral : 5.348 35.269 3101 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 1.92 % Allowed : 6.30 % Favored : 91.78 % 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: -0.37 (0.15), residues: 2844 helix: 0.35 (0.19), residues: 726 sheet: 0.19 (0.21), residues: 576 loop : -0.66 (0.14), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1039 TYR 0.053 0.003 TYR B 380 PHE 0.040 0.004 PHE A 543 TRP 0.019 0.003 TRP B1102 HIS 0.009 0.002 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.29 (24198) covalent geometry : angle 0.95290 / 0.48 (32913) SS BOND : bond 0.01366 / 0.99 ( 36) SS BOND : angle 1.58114 / 1.05 ( 72) hydrogen bonds : bond 0.05333 / 3.46 ( 988) hydrogen bonds : angle 6.49938 / 4.52 ( 2748) Misc. bond : bond 0.01792 / 0.85 ( 3) link_BETA1-4 : bond 0.01110 / 0.64 ( 15) link_BETA1-4 : angle 1.80362 / 1.38 ( 45) link_NAG-ASN : bond 0.00898 / 0.59 ( 32) link_NAG-ASN : angle 3.76009 / 2.60 ( 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 464 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 415 time to evaluate : 0.797 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: A 119 ILE cc_start: 0.5103 (OUTLIER) cc_final: 0.4878 (pt) REVERT: A 312 ILE cc_start: 0.4639 (OUTLIER) cc_final: 0.4372 (tt) REVERT: A 327 VAL cc_start: 0.5888 (t) cc_final: 0.5340 (p) REVERT: A 516 GLU cc_start: 0.5754 (pp20) cc_final: 0.5420 (mp0) REVERT: A 558 LYS cc_start: 0.5840 (mppt) cc_final: 0.5432 (mtmm) REVERT: A 748 GLU cc_start: 0.6722 (mp0) cc_final: 0.6519 (mp0) REVERT: A 764 ASN cc_start: 0.6875 (m110) cc_final: 0.6556 (m110) REVERT: A 906 PHE cc_start: 0.6025 (m-80) cc_final: 0.5159 (m-80) REVERT: A 970 PHE cc_start: 0.6229 (m-80) cc_final: 0.4844 (m-10) REVERT: A 988 GLU cc_start: 0.6968 (pm20) cc_final: 0.6619 (pm20) REVERT: A 1000 ARG cc_start: 0.6805 (mtt180) cc_final: 0.5781 (ttm170) REVERT: A 1067 TYR cc_start: 0.6192 (t80) cc_final: 0.5810 (t80) REVERT: B 30 ASN cc_start: 0.4188 (t0) cc_final: 0.3813 (p0) REVERT: B 121 ASN cc_start: 0.5706 (OUTLIER) cc_final: 0.4974 (p0) REVERT: B 224 GLU cc_start: 0.5904 (pm20) cc_final: 0.5461 (mp0) REVERT: B 285 ILE cc_start: 0.6648 (mt) cc_final: 0.6336 (mt) REVERT: B 543 PHE cc_start: 0.5238 (m-80) cc_final: 0.4803 (m-10) REVERT: B 900 MET cc_start: 0.4909 (mmt) cc_final: 0.4670 (mmp) REVERT: B 979 ASP cc_start: 0.6640 (m-30) cc_final: 0.6426 (m-30) REVERT: B 1000 ARG cc_start: 0.5290 (mpt180) cc_final: 0.4773 (mmt-90) REVERT: C 269 TYR cc_start: 0.6692 (m-80) cc_final: 0.6490 (m-80) REVERT: C 768 THR cc_start: 0.6835 (m) cc_final: 0.5612 (p) REVERT: C 777 ASN cc_start: 0.5158 (m-40) cc_final: 0.4913 (m-40) REVERT: C 963 VAL cc_start: 0.6352 (t) cc_final: 0.5474 (p) REVERT: C 1004 LEU cc_start: 0.5559 (OUTLIER) cc_final: 0.4811 (mt) REVERT: C 1006 THR cc_start: 0.7044 (m) cc_final: 0.6840 (p) REVERT: C 1008 VAL cc_start: 0.5684 (t) cc_final: 0.4514 (m) REVERT: C 1029 MET cc_start: 0.6383 (tmm) cc_final: 0.6141 (tmm) outliers start: 49 outliers final: 20 residues processed: 438 average time/residue: 0.1544 time to fit residues: 106.0590 Evaluate side-chains 360 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 336 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 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 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: 0.0970 chunk 150 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 chunk 244 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 59 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 170 optimal weight: 0.6980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN A1048 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B 992 GLN B1011 GLN C 603 ASN C 607 GLN C1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.167699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137973 restraints weight = 36996.805| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.94 r_work: 0.3547 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5558 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 24284 Z= 0.182 Angle : 0.733 23.802 33126 Z= 0.367 Chirality : 0.048 0.388 3932 Planarity : 0.005 0.061 4164 Dihedral : 4.626 28.873 3099 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.43 % Allowed : 9.94 % Favored : 87.64 % 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: -0.12 (0.15), residues: 2844 helix: 0.98 (0.19), residues: 729 sheet: 0.17 (0.20), residues: 585 loop : -0.67 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 646 TYR 0.023 0.002 TYR B1067 PHE 0.026 0.002 PHE B 306 TRP 0.024 0.002 TRP C 104 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (24198) covalent geometry : angle 0.68977 / 0.35 (32913) SS BOND : bond 0.00921 / 0.62 ( 36) SS BOND : angle 2.85446 / 1.91 ( 72) hydrogen bonds : bond 0.04824 / 3.14 ( 988) hydrogen bonds : angle 6.01376 / 4.16 ( 2748) Misc. bond : bond 0.00080 / 0.04 ( 3) link_BETA1-4 : bond 0.00483 / 0.30 ( 15) link_BETA1-4 : angle 1.38119 / 0.98 ( 45) link_NAG-ASN : bond 0.01168 / 0.81 ( 32) link_NAG-ASN : angle 3.90225 / 2.63 ( 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 456 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 394 time to evaluate : 0.835 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 327 VAL cc_start: 0.6498 (t) cc_final: 0.6161 (p) REVERT: A 664 ILE cc_start: 0.6466 (tp) cc_final: 0.6120 (tt) REVERT: A 714 ILE cc_start: 0.6384 (OUTLIER) cc_final: 0.5853 (mt) REVERT: A 764 ASN cc_start: 0.7200 (m110) cc_final: 0.6998 (m-40) REVERT: A 869 MET cc_start: 0.7249 (ttp) cc_final: 0.7005 (ttm) REVERT: A 887 THR cc_start: 0.6184 (m) cc_final: 0.5771 (m) REVERT: A 906 PHE cc_start: 0.6336 (m-80) cc_final: 0.4322 (m-10) REVERT: A 919 ASN cc_start: 0.6103 (m110) cc_final: 0.5746 (m110) REVERT: A 1000 ARG cc_start: 0.7216 (mtt180) cc_final: 0.6762 (mtt180) REVERT: A 1005 GLN cc_start: 0.7665 (tm-30) cc_final: 0.7370 (tt0) REVERT: A 1120 THR cc_start: 0.4714 (p) cc_final: 0.4318 (t) REVERT: B 206 LYS cc_start: 0.7796 (tptt) cc_final: 0.7480 (tptt) REVERT: B 224 GLU cc_start: 0.5817 (pm20) cc_final: 0.5465 (mp0) REVERT: B 285 ILE cc_start: 0.7337 (mt) cc_final: 0.6932 (mm) REVERT: B 428 ASP cc_start: 0.5984 (t0) cc_final: 0.5695 (t0) REVERT: B 543 PHE cc_start: 0.5708 (m-80) cc_final: 0.4826 (m-10) REVERT: B 730 SER cc_start: 0.5527 (m) cc_final: 0.4862 (p) REVERT: B 731 MET cc_start: 0.7265 (mtm) cc_final: 0.6333 (mtp) REVERT: B 900 MET cc_start: 0.5012 (mmt) cc_final: 0.4690 (mmp) REVERT: B 906 PHE cc_start: 0.4471 (m-80) cc_final: 0.3548 (m-10) REVERT: B 1000 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.5396 (mmm-85) REVERT: C 115 GLN cc_start: 0.4232 (mp10) cc_final: 0.3746 (tt0) REVERT: C 269 TYR cc_start: 0.6967 (m-80) cc_final: 0.6738 (m-80) REVERT: C 271 GLN cc_start: 0.6188 (pm20) cc_final: 0.5802 (pm20) REVERT: C 275 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7713 (t80) REVERT: C 765 ARG cc_start: 0.6619 (tpp80) cc_final: 0.6079 (tpp80) REVERT: C 984 LEU cc_start: 0.6476 (mt) cc_final: 0.6223 (mm) REVERT: C 995 ARG cc_start: 0.7153 (mtt90) cc_final: 0.6894 (mtm-85) REVERT: C 1029 MET cc_start: 0.6901 (tmm) cc_final: 0.6552 (tpp) REVERT: C 1102 TRP cc_start: 0.4700 (m100) cc_final: 0.4216 (m100) REVERT: C 1111 GLU cc_start: 0.6234 (tm-30) cc_final: 0.5754 (tm-30) outliers start: 62 outliers final: 27 residues processed: 419 average time/residue: 0.1671 time to fit residues: 110.3598 Evaluate side-chains 379 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 349 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 119 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 582 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1065 VAL 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 596 SER Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 916 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: 0.9990 chunk 191 optimal weight: 0.5980 chunk 156 optimal weight: 0.9990 chunk 268 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 289 optimal weight: 0.5980 chunk 288 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 285 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 91 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN A1064 HIS B 370 ASN B 762 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 607 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.169143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.138958 restraints weight = 37265.723| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.00 r_work: 0.3564 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.8495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.148 24284 Z= 0.252 Angle : 0.831 20.591 33126 Z= 0.417 Chirality : 0.053 0.634 3932 Planarity : 0.006 0.096 4164 Dihedral : 4.994 30.700 3099 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.64 % Allowed : 12.44 % Favored : 83.92 % Cbeta Deviations : 0.04 % 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: -0.36 (0.15), residues: 2844 helix: 0.61 (0.19), residues: 729 sheet: 0.22 (0.21), residues: 579 loop : -0.81 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1039 TYR 0.032 0.002 TYR B1067 PHE 0.027 0.002 PHE B 58 TRP 0.014 0.002 TRP C 64 HIS 0.012 0.002 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.25 (24198) covalent geometry : angle 0.79934 / 0.41 (32913) SS BOND : bond 0.02181 / 1.19 ( 36) SS BOND : angle 2.85520 / 1.89 ( 72) hydrogen bonds : bond 0.04643 / 3.01 ( 988) hydrogen bonds : angle 5.94594 / 4.09 ( 2748) Misc. bond : bond 0.01443 / 0.69 ( 3) link_BETA1-4 : bond 0.00506 / 0.27 ( 15) link_BETA1-4 : angle 1.24366 / 0.82 ( 45) link_NAG-ASN : bond 0.01054 / 0.70 ( 32) link_NAG-ASN : angle 3.51829 / 2.38 ( 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 605 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 512 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 119 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.6553 (mt) REVERT: A 238 PHE cc_start: 0.7176 (p90) cc_final: 0.6960 (p90) REVERT: A 266 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6937 (m-10) REVERT: A 327 VAL cc_start: 0.7026 (t) cc_final: 0.6755 (p) REVERT: A 565 PHE cc_start: 0.6853 (m-80) cc_final: 0.6652 (m-80) REVERT: A 664 ILE cc_start: 0.7512 (tp) cc_final: 0.7086 (tt) REVERT: A 714 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7275 (mt) REVERT: A 729 VAL cc_start: 0.8130 (t) cc_final: 0.7146 (p) REVERT: A 731 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7914 (ptt) REVERT: A 752 LEU cc_start: 0.8918 (tp) cc_final: 0.8664 (tt) REVERT: A 759 PHE cc_start: 0.8330 (m-10) cc_final: 0.8101 (m-80) REVERT: A 765 ARG cc_start: 0.7792 (ptm-80) cc_final: 0.7408 (ttm-80) REVERT: A 868 GLU cc_start: 0.7166 (mp0) cc_final: 0.6763 (mp0) REVERT: A 869 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7857 (ttm) REVERT: A 985 ASP cc_start: 0.7440 (p0) cc_final: 0.6899 (p0) REVERT: A 990 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 1008 VAL cc_start: 0.8628 (p) cc_final: 0.8222 (t) REVERT: A 1058 HIS cc_start: 0.7287 (m-70) cc_final: 0.7080 (m170) REVERT: A 1073 LYS cc_start: 0.8017 (tttp) cc_final: 0.7814 (tptp) REVERT: B 224 GLU cc_start: 0.6253 (pm20) cc_final: 0.4460 (mp0) REVERT: B 305 SER cc_start: 0.8483 (t) cc_final: 0.8151 (p) REVERT: B 388 ASN cc_start: 0.7423 (p0) cc_final: 0.7205 (m-40) REVERT: B 392 PHE cc_start: 0.7997 (m-80) cc_final: 0.7425 (m-80) REVERT: B 428 ASP cc_start: 0.6281 (t0) cc_final: 0.5970 (t0) REVERT: B 514 SER cc_start: 0.8153 (t) cc_final: 0.7685 (p) REVERT: B 543 PHE cc_start: 0.6760 (m-80) cc_final: 0.5891 (m-80) REVERT: B 612 TYR cc_start: 0.7461 (m-80) cc_final: 0.7246 (m-80) REVERT: B 735 SER cc_start: 0.8911 (p) cc_final: 0.8573 (p) REVERT: B 736 VAL cc_start: 0.7975 (t) cc_final: 0.7772 (m) REVERT: B 767 LEU cc_start: 0.6714 (mt) cc_final: 0.6500 (mp) REVERT: B 797 PHE cc_start: 0.6780 (m-80) cc_final: 0.6528 (m-80) REVERT: B 900 MET cc_start: 0.6265 (mmt) cc_final: 0.6054 (mmm) REVERT: B 902 MET cc_start: 0.4373 (OUTLIER) cc_final: 0.3530 (ttt) REVERT: B 906 PHE cc_start: 0.6076 (m-10) cc_final: 0.4779 (m-80) REVERT: B 995 ARG cc_start: 0.7790 (ttm170) cc_final: 0.7430 (ttm170) REVERT: B 1000 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7568 (mmt90) REVERT: B 1029 MET cc_start: 0.5983 (tpt) cc_final: 0.5752 (tpt) REVERT: C 32 PHE cc_start: 0.6379 (m-80) cc_final: 0.6137 (m-80) REVERT: C 58 PHE cc_start: 0.4977 (OUTLIER) cc_final: 0.4505 (m-80) REVERT: C 269 TYR cc_start: 0.7281 (m-80) cc_final: 0.7059 (m-80) REVERT: C 273 ARG cc_start: 0.7338 (mtp180) cc_final: 0.6849 (mtp180) REVERT: C 327 VAL cc_start: 0.7791 (t) cc_final: 0.7446 (m) REVERT: C 365 TYR cc_start: 0.7433 (m-80) cc_final: 0.7049 (m-80) REVERT: C 537 LYS cc_start: 0.7619 (ttpt) cc_final: 0.7327 (ttpt) REVERT: C 612 TYR cc_start: 0.7919 (m-80) cc_final: 0.7703 (m-80) REVERT: C 740 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7197 (mmm) REVERT: C 756 TYR cc_start: 0.7918 (m-80) cc_final: 0.7635 (m-80) REVERT: C 762 GLN cc_start: 0.6842 (mm110) cc_final: 0.6629 (mm110) REVERT: C 984 LEU cc_start: 0.7419 (mt) cc_final: 0.7174 (mp) REVERT: C 1014 ARG cc_start: 0.7844 (ttp-110) cc_final: 0.7605 (ttm-80) outliers start: 93 outliers final: 44 residues processed: 558 average time/residue: 0.1621 time to fit residues: 143.3159 Evaluate side-chains 489 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 436 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 267 VAL 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 719 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 91 TYR 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 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1094 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: 0.5980 chunk 134 optimal weight: 0.1980 chunk 266 optimal weight: 0.6980 chunk 281 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 226 optimal weight: 0.9980 chunk 49 optimal weight: 0.0980 chunk 13 optimal weight: 0.5980 chunk 284 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 239 GLN A 755 GLN A 764 ASN A1005 GLN A1064 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN B 957 GLN B1108 ASN C 30 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1002 GLN C1005 GLN C1135 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.167981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.137281 restraints weight = 36852.906| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.98 r_work: 0.3539 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.9910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 24284 Z= 0.188 Angle : 0.738 21.716 33126 Z= 0.367 Chirality : 0.049 0.314 3932 Planarity : 0.005 0.071 4164 Dihedral : 4.782 28.445 3099 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.52 % Allowed : 15.65 % Favored : 80.83 % 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: -0.12 (0.15), residues: 2844 helix: 1.08 (0.20), residues: 720 sheet: 0.04 (0.20), residues: 624 loop : -0.67 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 357 TYR 0.023 0.002 TYR B1067 PHE 0.036 0.002 PHE C 800 TRP 0.017 0.002 TRP B1102 HIS 0.008 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (24198) covalent geometry : angle 0.69513 / 0.36 (32913) SS BOND : bond 0.01073 / 0.58 ( 36) SS BOND : angle 2.92432 / 1.81 ( 72) hydrogen bonds : bond 0.04393 / 2.84 ( 988) hydrogen bonds : angle 5.75153 / 3.98 ( 2748) Misc. bond : bond 0.01288 / 0.61 ( 3) link_BETA1-4 : bond 0.00480 / 0.27 ( 15) link_BETA1-4 : angle 1.77306 / 1.11 ( 45) link_NAG-ASN : bond 0.01042 / 0.76 ( 32) link_NAG-ASN : angle 3.76831 / 2.55 ( 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 594 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 504 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.7283 (pm20) cc_final: 0.6809 (pm20) REVERT: A 236 THR cc_start: 0.8302 (t) cc_final: 0.7989 (m) REVERT: A 238 PHE cc_start: 0.7294 (p90) cc_final: 0.7037 (p90) REVERT: A 266 TYR cc_start: 0.7605 (OUTLIER) cc_final: 0.7023 (m-10) REVERT: A 354 ASN cc_start: 0.7758 (t0) cc_final: 0.7556 (t0) REVERT: A 515 PHE cc_start: 0.8235 (m-80) cc_final: 0.8006 (m-10) REVERT: A 537 LYS cc_start: 0.8315 (mtmm) cc_final: 0.8074 (mttp) REVERT: A 565 PHE cc_start: 0.6858 (m-80) cc_final: 0.6657 (m-80) REVERT: A 710 ASN cc_start: 0.6601 (m-40) cc_final: 0.5887 (p0) REVERT: A 765 ARG cc_start: 0.7902 (ptm-80) cc_final: 0.7522 (ttm-80) REVERT: A 869 MET cc_start: 0.8409 (ttp) cc_final: 0.8124 (mtm) REVERT: A 900 MET cc_start: 0.7470 (mmt) cc_final: 0.7246 (mmt) REVERT: A 918 GLU cc_start: 0.7665 (mp0) cc_final: 0.7021 (mp0) REVERT: A 985 ASP cc_start: 0.7363 (p0) cc_final: 0.6904 (p0) REVERT: A 1023 ASN cc_start: 0.8145 (t0) cc_final: 0.7633 (m-40) REVERT: A 1050 MET cc_start: 0.8374 (pmm) cc_final: 0.8159 (pmm) REVERT: B 224 GLU cc_start: 0.6229 (pm20) cc_final: 0.4525 (mp0) REVERT: B 285 ILE cc_start: 0.8065 (mt) cc_final: 0.7781 (mm) REVERT: B 305 SER cc_start: 0.8645 (t) cc_final: 0.8324 (p) REVERT: B 392 PHE cc_start: 0.7865 (m-80) cc_final: 0.7039 (m-80) REVERT: B 394 ASN cc_start: 0.7855 (p0) cc_final: 0.7612 (p0) REVERT: B 428 ASP cc_start: 0.6535 (t0) cc_final: 0.6196 (t0) REVERT: B 514 SER cc_start: 0.8538 (t) cc_final: 0.7983 (p) REVERT: B 515 PHE cc_start: 0.7940 (m-80) cc_final: 0.7579 (m-10) REVERT: B 651 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7399 (mm) REVERT: B 735 SER cc_start: 0.8836 (p) cc_final: 0.8557 (p) REVERT: B 1000 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7689 (mtt90) REVERT: B 1029 MET cc_start: 0.7086 (tpt) cc_final: 0.6728 (tpp) REVERT: B 1123 SER cc_start: 0.7217 (t) cc_final: 0.6999 (t) REVERT: C 53 ASP cc_start: 0.6258 (t70) cc_final: 0.5799 (t70) REVERT: C 58 PHE cc_start: 0.4828 (OUTLIER) cc_final: 0.4459 (m-10) REVERT: C 307 THR cc_start: 0.8764 (m) cc_final: 0.8316 (p) REVERT: C 327 VAL cc_start: 0.7919 (t) cc_final: 0.7635 (m) REVERT: C 365 TYR cc_start: 0.7305 (m-80) cc_final: 0.6891 (m-80) REVERT: C 537 LYS cc_start: 0.7800 (ttpt) cc_final: 0.7448 (ttpt) REVERT: C 756 TYR cc_start: 0.8307 (m-80) cc_final: 0.7642 (m-80) REVERT: C 990 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6771 (mm-30) REVERT: C 995 ARG cc_start: 0.7684 (mtt90) cc_final: 0.7451 (mtt90) outliers start: 90 outliers final: 44 residues processed: 549 average time/residue: 0.1652 time to fit residues: 143.0134 Evaluate side-chains 497 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 449 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL 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 358 ILE Chi-restraints excluded: chain C residue 385 THR 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 617 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU 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: 1.9990 chunk 229 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 157 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 235 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 chunk 86 optimal weight: 0.0670 chunk 145 optimal weight: 0.6980 chunk 256 optimal weight: 0.5980 chunk 261 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN A 394 ASN A 755 GLN A 762 GLN A 872 GLN A1005 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 901 GLN B 949 GLN C 115 GLN C 580 GLN C 710 ASN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.165997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134708 restraints weight = 37263.492| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 3.03 r_work: 0.3489 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 1.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 24284 Z= 0.210 Angle : 0.761 19.802 33126 Z= 0.384 Chirality : 0.050 0.309 3932 Planarity : 0.006 0.190 4164 Dihedral : 4.940 26.672 3099 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.87 % Allowed : 17.33 % Favored : 78.79 % 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: -0.28 (0.15), residues: 2844 helix: 1.03 (0.20), residues: 738 sheet: -0.05 (0.20), residues: 642 loop : -0.85 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 237 TYR 0.030 0.002 TYR C 380 PHE 0.044 0.002 PHE B 58 TRP 0.011 0.002 TRP C 104 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (24198) covalent geometry : angle 0.72850 / 0.38 (32913) SS BOND : bond 0.00895 / 0.52 ( 36) SS BOND : angle 2.61440 / 1.56 ( 72) hydrogen bonds : bond 0.04730 / 3.07 ( 988) hydrogen bonds : angle 5.66158 / 3.90 ( 2748) Misc. bond : bond 0.01034 / 0.49 ( 3) link_BETA1-4 : bond 0.00552 / 0.27 ( 15) link_BETA1-4 : angle 1.34044 / 0.84 ( 45) link_NAG-ASN : bond 0.00938 / 0.63 ( 32) link_NAG-ASN : angle 3.43125 / 2.31 ( 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 628 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 529 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6963 (tp40) cc_final: 0.6651 (tp40) REVERT: A 236 THR cc_start: 0.7934 (t) cc_final: 0.7583 (t) REVERT: A 238 PHE cc_start: 0.7564 (p90) cc_final: 0.7293 (p90) REVERT: A 266 TYR cc_start: 0.7801 (OUTLIER) cc_final: 0.7531 (m-80) REVERT: A 299 THR cc_start: 0.8176 (m) cc_final: 0.7808 (p) REVERT: A 329 PHE cc_start: 0.7419 (m-80) cc_final: 0.7181 (m-10) REVERT: A 406 GLU cc_start: 0.6678 (pm20) cc_final: 0.6425 (pm20) REVERT: A 537 LYS cc_start: 0.8226 (mtmm) cc_final: 0.8008 (mtpp) REVERT: A 539 VAL cc_start: 0.8431 (m) cc_final: 0.8215 (m) REVERT: A 646 ARG cc_start: 0.7580 (mmp80) cc_final: 0.7271 (mmp80) REVERT: A 650 LEU cc_start: 0.7768 (mp) cc_final: 0.7390 (mt) REVERT: A 732 THR cc_start: 0.8704 (m) cc_final: 0.8446 (p) REVERT: A 759 PHE cc_start: 0.8313 (m-10) cc_final: 0.8078 (m-80) REVERT: A 765 ARG cc_start: 0.7920 (ptm-80) cc_final: 0.7523 (ttm-80) REVERT: A 773 GLU cc_start: 0.8225 (tp30) cc_final: 0.7801 (tp30) REVERT: A 780 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7472 (pp20) REVERT: A 869 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8213 (mtm) REVERT: A 872 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: A 918 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: A 1023 ASN cc_start: 0.8163 (t0) cc_final: 0.7782 (m-40) REVERT: A 1034 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8109 (mt) REVERT: A 1048 HIS cc_start: 0.7912 (t-90) cc_final: 0.7572 (t-90) REVERT: B 239 GLN cc_start: 0.7972 (tt0) cc_final: 0.7526 (tm-30) REVERT: B 281 GLU cc_start: 0.5629 (tp30) cc_final: 0.5366 (tp30) REVERT: B 305 SER cc_start: 0.8845 (t) cc_final: 0.8440 (p) REVERT: B 319 ARG cc_start: 0.7094 (ttm-80) cc_final: 0.6777 (ttm-80) REVERT: B 357 ARG cc_start: 0.7164 (mpt180) cc_final: 0.6868 (mpt180) REVERT: B 364 ASP cc_start: 0.6114 (t0) cc_final: 0.5644 (t0) REVERT: B 392 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: B 394 ASN cc_start: 0.7924 (p0) cc_final: 0.7654 (p0) REVERT: B 428 ASP cc_start: 0.6805 (t0) cc_final: 0.6571 (t0) REVERT: B 535 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8129 (mtmt) REVERT: B 644 GLN cc_start: 0.7247 (mm-40) cc_final: 0.6801 (mm-40) REVERT: B 752 LEU cc_start: 0.8327 (tt) cc_final: 0.8054 (mt) REVERT: B 762 GLN cc_start: 0.7754 (tp40) cc_final: 0.7101 (tp40) REVERT: B 765 ARG cc_start: 0.7777 (ttm110) cc_final: 0.7411 (ttm110) REVERT: B 806 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7996 (mt) REVERT: B 988 GLU cc_start: 0.7966 (mp0) cc_final: 0.7748 (mp0) REVERT: B 994 ASP cc_start: 0.7580 (m-30) cc_final: 0.7340 (m-30) REVERT: B 1000 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7803 (mtt90) REVERT: B 1030 SER cc_start: 0.8098 (m) cc_final: 0.7791 (p) REVERT: B 1038 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8166 (tppt) REVERT: B 1123 SER cc_start: 0.7950 (t) cc_final: 0.7714 (t) REVERT: C 91 TYR cc_start: 0.7751 (t80) cc_final: 0.7468 (t80) REVERT: C 271 GLN cc_start: 0.7254 (pm20) cc_final: 0.7035 (pm20) REVERT: C 305 SER cc_start: 0.8806 (t) cc_final: 0.8562 (m) REVERT: C 365 TYR cc_start: 0.7489 (m-80) cc_final: 0.7065 (m-80) REVERT: C 516 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.6335 (tt0) REVERT: C 537 LYS cc_start: 0.7888 (ttpt) cc_final: 0.7619 (ttmm) REVERT: C 656 VAL cc_start: 0.7825 (OUTLIER) cc_final: 0.7539 (p) REVERT: C 657 ASN cc_start: 0.7517 (m-40) cc_final: 0.7201 (m-40) REVERT: C 660 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: C 697 MET cc_start: 0.7929 (ttt) cc_final: 0.7683 (ttm) REVERT: C 756 TYR cc_start: 0.8641 (m-80) cc_final: 0.8333 (m-80) REVERT: C 764 ASN cc_start: 0.8177 (t0) cc_final: 0.7967 (m-40) REVERT: C 859 THR cc_start: 0.8399 (p) cc_final: 0.8189 (t) REVERT: C 902 MET cc_start: 0.7677 (mmm) cc_final: 0.7076 (mmm) REVERT: C 1072 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7512 (pm20) outliers start: 99 outliers final: 49 residues processed: 577 average time/residue: 0.1665 time to fit residues: 151.0611 Evaluate side-chains 518 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 455 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1034 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 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 238 PHE 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 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 620 VAL 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 806 LEU 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 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1072 GLU 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: 0.0870 chunk 246 optimal weight: 0.7980 chunk 286 optimal weight: 0.8980 chunk 256 optimal weight: 0.7980 chunk 269 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 180 optimal weight: 0.1980 chunk 191 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN A 644 GLN A 762 GLN A 872 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 949 GLN B 969 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 314 GLN C 317 ASN C 804 GLN C1010 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.164048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131601 restraints weight = 36565.485| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.06 r_work: 0.3459 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 1.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 24284 Z= 0.189 Angle : 0.720 21.418 33126 Z= 0.360 Chirality : 0.049 0.676 3932 Planarity : 0.005 0.058 4164 Dihedral : 4.780 30.466 3099 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.64 % Allowed : 19.33 % Favored : 77.03 % 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: -0.20 (0.15), residues: 2844 helix: 1.15 (0.20), residues: 738 sheet: -0.03 (0.20), residues: 618 loop : -0.81 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C1107 TYR 0.026 0.002 TYR A1067 PHE 0.020 0.002 PHE B 58 TRP 0.008 0.001 TRP C 104 HIS 0.006 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (24198) covalent geometry : angle 0.67501 / 0.35 (32913) SS BOND : bond 0.00700 / 0.46 ( 36) SS BOND : angle 3.19266 / 2.01 ( 72) hydrogen bonds : bond 0.04568 / 2.97 ( 988) hydrogen bonds : angle 5.57082 / 3.87 ( 2748) Misc. bond : bond 0.00228 / 0.11 ( 3) link_BETA1-4 : bond 0.00585 / 0.30 ( 15) link_BETA1-4 : angle 1.54480 / 0.98 ( 45) link_NAG-ASN : bond 0.00780 / 0.54 ( 32) link_NAG-ASN : angle 3.76208 / 2.56 ( 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 614 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 521 time to evaluate : 0.921 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: 0.7156 (tp40) cc_final: 0.6956 (tp40) REVERT: A 236 THR cc_start: 0.8236 (t) cc_final: 0.8028 (m) REVERT: A 237 ARG cc_start: 0.7009 (mtp85) cc_final: 0.6669 (mtp85) REVERT: A 266 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: A 305 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.8193 (m) REVERT: A 329 PHE cc_start: 0.7335 (m-80) cc_final: 0.7119 (m-10) REVERT: A 608 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7741 (p) REVERT: A 732 THR cc_start: 0.8887 (m) cc_final: 0.8600 (p) REVERT: A 759 PHE cc_start: 0.8114 (m-10) cc_final: 0.7834 (m-80) REVERT: A 765 ARG cc_start: 0.7864 (ptm-80) cc_final: 0.7488 (ttm-80) REVERT: A 790 LYS cc_start: 0.7390 (pttt) cc_final: 0.7149 (mtmm) REVERT: A 823 PHE cc_start: 0.7633 (m-80) cc_final: 0.7060 (m-80) REVERT: A 887 THR cc_start: 0.8078 (m) cc_final: 0.7801 (p) REVERT: A 918 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: A 933 LYS cc_start: 0.7728 (mttm) cc_final: 0.7343 (mtmm) REVERT: A 976 VAL cc_start: 0.8660 (t) cc_final: 0.8279 (m) REVERT: A 987 PRO cc_start: 0.8828 (Cg_exo) cc_final: 0.8614 (Cg_endo) REVERT: A 988 GLU cc_start: 0.8247 (mp0) cc_final: 0.7804 (mp0) REVERT: A 1048 HIS cc_start: 0.8172 (t-90) cc_final: 0.7689 (t70) REVERT: B 169 GLU cc_start: 0.7366 (tt0) cc_final: 0.7159 (mt-10) REVERT: B 239 GLN cc_start: 0.8056 (tt0) cc_final: 0.7820 (tt0) REVERT: B 277 LEU cc_start: 0.8226 (mt) cc_final: 0.7924 (mm) REVERT: B 329 PHE cc_start: 0.8423 (m-10) cc_final: 0.8191 (m-80) REVERT: B 357 ARG cc_start: 0.7194 (mpt180) cc_final: 0.6863 (mpt180) REVERT: B 364 ASP cc_start: 0.6517 (t0) cc_final: 0.6111 (t0) REVERT: B 382 VAL cc_start: 0.8405 (t) cc_final: 0.8132 (p) REVERT: B 392 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7275 (m-80) REVERT: B 428 ASP cc_start: 0.6919 (t0) cc_final: 0.6704 (t0) REVERT: B 535 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8276 (mtmt) REVERT: B 726 ILE cc_start: 0.8406 (mm) cc_final: 0.8189 (mm) REVERT: B 765 ARG cc_start: 0.7863 (ttm110) cc_final: 0.7461 (ttm110) REVERT: B 790 LYS cc_start: 0.8453 (ttpp) cc_final: 0.8022 (ttmm) REVERT: B 795 LYS cc_start: 0.7553 (mmtm) cc_final: 0.7308 (mmtm) REVERT: B 894 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7827 (mp) REVERT: B 900 MET cc_start: 0.7608 (mmm) cc_final: 0.7202 (mpp) REVERT: B 933 LYS cc_start: 0.7592 (mttt) cc_final: 0.7359 (mmtm) REVERT: B 987 PRO cc_start: 0.8661 (Cg_exo) cc_final: 0.8359 (Cg_endo) REVERT: B 988 GLU cc_start: 0.7956 (mp0) cc_final: 0.7741 (mp0) REVERT: B 1000 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8009 (mtt-85) REVERT: B 1030 SER cc_start: 0.8416 (m) cc_final: 0.8016 (p) REVERT: B 1031 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7082 (mt-10) REVERT: B 1045 LYS cc_start: 0.8131 (ptmm) cc_final: 0.7680 (ttpt) REVERT: B 1119 ASN cc_start: 0.8157 (m-40) cc_final: 0.7680 (m110) REVERT: C 195 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7586 (ptmt) REVERT: C 305 SER cc_start: 0.8896 (t) cc_final: 0.8608 (m) REVERT: C 320 VAL cc_start: 0.8343 (t) cc_final: 0.8045 (m) REVERT: C 355 ARG cc_start: 0.8026 (mtm180) cc_final: 0.7703 (mmm160) REVERT: C 365 TYR cc_start: 0.7644 (m-80) cc_final: 0.7206 (m-80) REVERT: C 558 LYS cc_start: 0.8341 (mppt) cc_final: 0.8122 (mppt) REVERT: C 564 GLN cc_start: 0.6792 (mm110) cc_final: 0.6590 (mm110) REVERT: C 573 THR cc_start: 0.7891 (m) cc_final: 0.7568 (p) REVERT: C 656 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7694 (t) REVERT: C 657 ASN cc_start: 0.7654 (m-40) cc_final: 0.7288 (m-40) REVERT: C 660 TYR cc_start: 0.8147 (m-80) cc_final: 0.7654 (m-10) REVERT: C 736 VAL cc_start: 0.8184 (m) cc_final: 0.7956 (t) REVERT: C 756 TYR cc_start: 0.8846 (m-80) cc_final: 0.8546 (m-80) REVERT: C 779 GLN cc_start: 0.8549 (tp40) cc_final: 0.8161 (tm-30) REVERT: C 859 THR cc_start: 0.8546 (p) cc_final: 0.8242 (t) outliers start: 93 outliers final: 53 residues processed: 579 average time/residue: 0.1754 time to fit residues: 157.4056 Evaluate side-chains 538 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 475 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 434 ILE 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 608 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1096 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 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 LYS 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 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 697 MET 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 894 LEU Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 203 ILE 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 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 877 LEU 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: 2.9990 chunk 247 optimal weight: 0.0980 chunk 143 optimal weight: 0.0570 chunk 237 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 48 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 130 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN A1135 ASN B 536 ASN B 777 ASN B 895 GLN B 969 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 710 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.164686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132119 restraints weight = 36446.413| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.08 r_work: 0.3462 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 1.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 24284 Z= 0.138 Angle : 0.686 20.620 33126 Z= 0.342 Chirality : 0.047 0.494 3932 Planarity : 0.004 0.048 4164 Dihedral : 4.605 29.840 3099 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.01 % Allowed : 21.24 % Favored : 75.74 % 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: -0.09 (0.15), residues: 2844 helix: 1.40 (0.20), residues: 735 sheet: -0.08 (0.20), residues: 639 loop : -0.79 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 237 TYR 0.025 0.001 TYR A1067 PHE 0.030 0.002 PHE B 515 TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (24198) covalent geometry : angle 0.64556 / 0.33 (32913) SS BOND : bond 0.00802 / 0.58 ( 36) SS BOND : angle 2.82043 / 1.98 ( 72) hydrogen bonds : bond 0.04086 / 2.62 ( 988) hydrogen bonds : angle 5.44274 / 3.77 ( 2748) Misc. bond : bond 0.00193 / 0.09 ( 3) link_BETA1-4 : bond 0.00400 / 0.20 ( 15) link_BETA1-4 : angle 1.23110 / 0.86 ( 45) link_NAG-ASN : bond 0.00662 / 0.43 ( 32) link_NAG-ASN : angle 3.60119 / 2.46 ( 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 596 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 519 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7224 (tp40) cc_final: 0.7015 (tp40) REVERT: A 206 LYS cc_start: 0.7951 (tppt) cc_final: 0.7448 (tptp) REVERT: A 237 ARG cc_start: 0.6996 (mtp85) cc_final: 0.6635 (mtp85) REVERT: A 266 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: A 305 SER cc_start: 0.8493 (p) cc_final: 0.8275 (m) REVERT: A 329 PHE cc_start: 0.7304 (m-80) cc_final: 0.7098 (m-10) REVERT: A 608 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7735 (p) REVERT: A 650 LEU cc_start: 0.7686 (mp) cc_final: 0.7473 (mt) REVERT: A 693 ILE cc_start: 0.7950 (pt) cc_final: 0.7701 (pt) REVERT: A 732 THR cc_start: 0.8859 (m) cc_final: 0.8574 (p) REVERT: A 759 PHE cc_start: 0.8076 (m-10) cc_final: 0.7800 (m-80) REVERT: A 765 ARG cc_start: 0.7851 (ptm-80) cc_final: 0.7452 (ttm-80) REVERT: A 790 LYS cc_start: 0.7408 (pttt) cc_final: 0.7183 (mtmm) REVERT: A 823 PHE cc_start: 0.7691 (m-80) cc_final: 0.7109 (m-80) REVERT: A 887 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7773 (p) REVERT: A 918 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: A 933 LYS cc_start: 0.7960 (mttm) cc_final: 0.7538 (mtmm) REVERT: A 976 VAL cc_start: 0.8648 (t) cc_final: 0.8288 (m) REVERT: A 987 PRO cc_start: 0.8815 (Cg_exo) cc_final: 0.8595 (Cg_endo) REVERT: A 988 GLU cc_start: 0.8269 (mp0) cc_final: 0.7820 (mp0) REVERT: A 1118 ASP cc_start: 0.7016 (t0) cc_final: 0.6572 (t0) REVERT: B 206 LYS cc_start: 0.8007 (tptt) cc_final: 0.7646 (tptt) REVERT: B 239 GLN cc_start: 0.8016 (tt0) cc_final: 0.7461 (tm-30) REVERT: B 357 ARG cc_start: 0.7210 (mpt180) cc_final: 0.6868 (mpt180) REVERT: B 382 VAL cc_start: 0.8354 (t) cc_final: 0.8082 (p) REVERT: B 392 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: B 398 ASP cc_start: 0.7741 (m-30) cc_final: 0.7451 (m-30) REVERT: B 515 PHE cc_start: 0.8199 (m-10) cc_final: 0.7954 (m-10) REVERT: B 726 ILE cc_start: 0.8382 (mm) cc_final: 0.7913 (mm) REVERT: B 742 ILE cc_start: 0.8282 (mp) cc_final: 0.8052 (mp) REVERT: B 765 ARG cc_start: 0.7899 (ttm110) cc_final: 0.7500 (ttm110) REVERT: B 790 LYS cc_start: 0.8327 (ttpp) cc_final: 0.7966 (ttmm) REVERT: B 815 ARG cc_start: 0.7037 (ptp-170) cc_final: 0.6742 (ptt180) REVERT: B 888 PHE cc_start: 0.7958 (p90) cc_final: 0.7624 (p90) REVERT: B 900 MET cc_start: 0.7627 (mmm) cc_final: 0.7229 (mpp) REVERT: B 933 LYS cc_start: 0.7623 (mttt) cc_final: 0.7360 (mmtm) REVERT: B 949 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7529 (mm-40) REVERT: B 987 PRO cc_start: 0.8672 (Cg_exo) cc_final: 0.8300 (Cg_endo) REVERT: B 1000 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8170 (mmt90) REVERT: B 1030 SER cc_start: 0.8391 (m) cc_final: 0.8052 (p) REVERT: B 1045 LYS cc_start: 0.8177 (ptmm) cc_final: 0.7808 (mtpt) REVERT: B 1125 ASN cc_start: 0.7597 (m-40) cc_final: 0.7144 (t0) REVERT: C 240 THR cc_start: 0.8282 (m) cc_final: 0.7624 (t) REVERT: C 305 SER cc_start: 0.8905 (t) cc_final: 0.8633 (m) REVERT: C 320 VAL cc_start: 0.8291 (t) cc_final: 0.7917 (m) REVERT: C 355 ARG cc_start: 0.8180 (mtm180) cc_final: 0.7897 (mmm160) REVERT: C 365 TYR cc_start: 0.7522 (m-80) cc_final: 0.6827 (m-80) REVERT: C 515 PHE cc_start: 0.8313 (m-10) cc_final: 0.8101 (m-80) REVERT: C 573 THR cc_start: 0.7692 (m) cc_final: 0.7351 (p) REVERT: C 654 GLU cc_start: 0.7576 (tp30) cc_final: 0.7293 (tp30) REVERT: C 656 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7832 (t) REVERT: C 657 ASN cc_start: 0.7725 (m-40) cc_final: 0.7391 (m-40) REVERT: C 660 TYR cc_start: 0.8081 (m-80) cc_final: 0.7636 (m-10) REVERT: C 756 TYR cc_start: 0.8891 (m-80) cc_final: 0.8583 (m-80) REVERT: C 779 GLN cc_start: 0.8502 (tp40) cc_final: 0.8150 (tm-30) REVERT: C 859 THR cc_start: 0.8610 (p) cc_final: 0.8227 (t) REVERT: C 1029 MET cc_start: 0.8500 (tpp) cc_final: 0.8293 (ttp) outliers start: 77 outliers final: 49 residues processed: 566 average time/residue: 0.1718 time to fit residues: 150.0002 Evaluate side-chains 552 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 496 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 391 CYS 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 608 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1096 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 197 ILE Chi-restraints excluded: chain B residue 202 LYS 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 336 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 661 GLU 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 787 GLN Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 203 ILE 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 380 TYR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 1030 SER 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: 0.9990 chunk 65 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 276 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 281 optimal weight: 0.9990 chunk 242 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN A 317 ASN A 762 GLN A1083 HIS B 196 ASN B 317 ASN B 777 ASN B 801 ASN B 872 GLN B1010 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 804 GLN C1125 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.158981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126016 restraints weight = 36358.655| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.08 r_work: 0.3368 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 1.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 24284 Z= 0.245 Angle : 0.817 20.281 33126 Z= 0.415 Chirality : 0.052 0.410 3932 Planarity : 0.005 0.058 4164 Dihedral : 5.194 41.329 3099 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.33 % Allowed : 21.48 % 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: -0.51 (0.15), residues: 2844 helix: 0.90 (0.20), residues: 738 sheet: -0.28 (0.19), residues: 645 loop : -0.98 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 237 TYR 0.030 0.002 TYR A1067 PHE 0.052 0.003 PHE C1095 TRP 0.026 0.002 TRP B1102 HIS 0.013 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (24198) covalent geometry : angle 0.77625 / 0.40 (32913) SS BOND : bond 0.01043 / 0.59 ( 36) SS BOND : angle 3.58343 / 2.40 ( 72) hydrogen bonds : bond 0.05459 / 3.55 ( 988) hydrogen bonds : angle 5.66516 / 3.89 ( 2748) Misc. bond : bond 0.01977 / 0.94 ( 3) link_BETA1-4 : bond 0.00452 / 0.25 ( 15) link_BETA1-4 : angle 1.53195 / 1.08 ( 45) link_NAG-ASN : bond 0.00854 / 0.57 ( 32) link_NAG-ASN : angle 3.58211 / 2.46 ( 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 665 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 580 time to evaluate : 0.884 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: 0.7417 (tp40) cc_final: 0.7117 (tp40) REVERT: A 169 GLU cc_start: 0.7055 (tt0) cc_final: 0.6811 (mp0) REVERT: A 197 ILE cc_start: 0.8367 (tt) cc_final: 0.8137 (tt) REVERT: A 237 ARG cc_start: 0.7283 (mtp85) cc_final: 0.6995 (mtp85) REVERT: A 266 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: A 281 GLU cc_start: 0.7235 (tp30) cc_final: 0.6790 (tp30) REVERT: A 378 LYS cc_start: 0.7985 (mttt) cc_final: 0.7746 (mttt) REVERT: A 429 PHE cc_start: 0.7868 (t80) cc_final: 0.7561 (t80) REVERT: A 578 ASP cc_start: 0.7917 (t0) cc_final: 0.7556 (t0) REVERT: A 661 GLU cc_start: 0.7411 (pt0) cc_final: 0.7204 (pp20) REVERT: A 663 ASP cc_start: 0.7368 (t0) cc_final: 0.7132 (t0) REVERT: A 759 PHE cc_start: 0.8139 (m-10) cc_final: 0.7937 (m-80) REVERT: A 765 ARG cc_start: 0.8123 (ptm-80) cc_final: 0.7863 (mtm110) REVERT: A 790 LYS cc_start: 0.7917 (pttt) cc_final: 0.7658 (mtmm) REVERT: A 931 ILE cc_start: 0.8189 (mm) cc_final: 0.7952 (mm) REVERT: A 949 GLN cc_start: 0.7568 (tp40) cc_final: 0.7233 (tp40) REVERT: A 976 VAL cc_start: 0.8883 (t) cc_final: 0.8440 (m) REVERT: A 987 PRO cc_start: 0.8850 (Cg_exo) cc_final: 0.8516 (Cg_endo) REVERT: B 52 GLN cc_start: 0.7964 (mm110) cc_final: 0.7734 (tp40) REVERT: B 135 PHE cc_start: 0.4991 (m-80) cc_final: 0.4709 (m-80) REVERT: B 206 LYS cc_start: 0.7969 (tptt) cc_final: 0.7763 (tptt) REVERT: B 237 ARG cc_start: 0.7204 (mtp85) cc_final: 0.6810 (mtp85) REVERT: B 239 GLN cc_start: 0.8270 (tt0) cc_final: 0.8005 (tt0) REVERT: B 240 THR cc_start: 0.8149 (m) cc_final: 0.7949 (t) REVERT: B 274 THR cc_start: 0.6781 (t) cc_final: 0.6411 (m) REVERT: B 281 GLU cc_start: 0.6497 (tp30) cc_final: 0.6088 (tp30) REVERT: B 289 VAL cc_start: 0.7916 (t) cc_final: 0.7537 (m) REVERT: B 290 ASP cc_start: 0.7506 (p0) cc_final: 0.7016 (t70) REVERT: B 307 THR cc_start: 0.8056 (m) cc_final: 0.7718 (p) REVERT: B 357 ARG cc_start: 0.7263 (mpt180) cc_final: 0.6923 (mpt180) REVERT: B 365 TYR cc_start: 0.7795 (m-80) cc_final: 0.7113 (m-80) REVERT: B 382 VAL cc_start: 0.8602 (t) cc_final: 0.8376 (p) REVERT: B 398 ASP cc_start: 0.8242 (m-30) cc_final: 0.7780 (m-30) REVERT: B 567 ARG cc_start: 0.8012 (tpp80) cc_final: 0.7582 (ttm-80) REVERT: B 651 ILE cc_start: 0.8668 (mt) cc_final: 0.8436 (mt) REVERT: B 661 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: B 707 TYR cc_start: 0.8360 (t80) cc_final: 0.7901 (t80) REVERT: B 748 GLU cc_start: 0.6676 (pm20) cc_final: 0.6322 (pm20) REVERT: B 765 ARG cc_start: 0.7950 (ttm110) cc_final: 0.7477 (ttm110) REVERT: B 779 GLN cc_start: 0.8305 (tp40) cc_final: 0.7941 (tp40) REVERT: B 790 LYS cc_start: 0.8262 (ttpp) cc_final: 0.8029 (ttmm) REVERT: B 815 ARG cc_start: 0.7926 (ptp-170) cc_final: 0.7692 (ptt180) REVERT: B 888 PHE cc_start: 0.8281 (p90) cc_final: 0.8013 (p90) REVERT: B 900 MET cc_start: 0.7985 (mmm) cc_final: 0.7700 (mpp) REVERT: B 933 LYS cc_start: 0.8047 (mttt) cc_final: 0.7679 (mmtm) REVERT: B 936 ASP cc_start: 0.7681 (m-30) cc_final: 0.7480 (m-30) REVERT: B 954 GLN cc_start: 0.7593 (mt0) cc_final: 0.7168 (mt0) REVERT: B 1000 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7864 (mtt90) REVERT: B 1038 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8544 (mmmm) REVERT: B 1045 LYS cc_start: 0.8298 (ptmm) cc_final: 0.8051 (mtpt) REVERT: C 195 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7737 (ptmt) REVERT: C 240 THR cc_start: 0.8368 (m) cc_final: 0.7871 (t) REVERT: C 271 GLN cc_start: 0.7677 (pm20) cc_final: 0.7350 (pm20) REVERT: C 273 ARG cc_start: 0.7852 (ptm160) cc_final: 0.7529 (mtm110) REVERT: C 278 LYS cc_start: 0.8067 (tttt) cc_final: 0.7820 (tttt) REVERT: C 299 THR cc_start: 0.8286 (t) cc_final: 0.8086 (t) REVERT: C 305 SER cc_start: 0.8952 (t) cc_final: 0.8643 (m) REVERT: C 308 VAL cc_start: 0.7847 (t) cc_final: 0.7600 (t) REVERT: C 320 VAL cc_start: 0.8679 (t) cc_final: 0.8323 (m) REVERT: C 358 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8255 (mt) REVERT: C 395 VAL cc_start: 0.7734 (t) cc_final: 0.7355 (p) REVERT: C 428 ASP cc_start: 0.7527 (p0) cc_final: 0.7171 (p0) REVERT: C 529 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7937 (mmtt) REVERT: C 551 VAL cc_start: 0.8730 (m) cc_final: 0.8487 (p) REVERT: C 573 THR cc_start: 0.8010 (m) cc_final: 0.7705 (p) REVERT: C 577 ARG cc_start: 0.8487 (mtt-85) cc_final: 0.8187 (ttm170) REVERT: C 610 VAL cc_start: 0.8702 (t) cc_final: 0.8491 (t) REVERT: C 654 GLU cc_start: 0.7647 (tp30) cc_final: 0.7181 (tp30) REVERT: C 736 VAL cc_start: 0.8475 (m) cc_final: 0.8207 (t) REVERT: C 779 GLN cc_start: 0.8565 (tp40) cc_final: 0.8069 (tm-30) REVERT: C 784 GLN cc_start: 0.7893 (mt0) cc_final: 0.7647 (mt0) REVERT: C 914 ASN cc_start: 0.8118 (m-40) cc_final: 0.7864 (m110) REVERT: C 931 ILE cc_start: 0.7684 (mm) cc_final: 0.7362 (mm) REVERT: C 950 ASP cc_start: 0.7196 (t0) cc_final: 0.6855 (t0) REVERT: C 954 GLN cc_start: 0.7497 (mt0) cc_final: 0.7103 (mt0) REVERT: C 1005 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7951 (mm-40) REVERT: C 1014 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.7952 (ttm-80) REVERT: C 1073 LYS cc_start: 0.8484 (ptpp) cc_final: 0.8086 (mtpp) REVERT: C 1133 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8308 (m) outliers start: 85 outliers final: 52 residues processed: 631 average time/residue: 0.1785 time to fit residues: 171.5618 Evaluate side-chains 592 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 533 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1031 GLU 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 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 661 GLU 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 872 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1133 VAL 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: 0.5980 chunk 179 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 241 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 187 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 10 optimal weight: 0.0470 chunk 82 optimal weight: 0.2980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN A1135 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 ASN B1048 HIS ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 580 GLN C 710 ASN C 804 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.159709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.126468 restraints weight = 36067.068| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.08 r_work: 0.3376 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 1.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24284 Z= 0.182 Angle : 0.742 20.426 33126 Z= 0.376 Chirality : 0.048 0.383 3932 Planarity : 0.005 0.052 4164 Dihedral : 4.879 38.098 3099 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.43 % Allowed : 22.85 % Favored : 74.73 % 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: -0.28 (0.15), residues: 2844 helix: 1.26 (0.20), residues: 738 sheet: -0.15 (0.19), residues: 672 loop : -0.96 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 237 TYR 0.030 0.002 TYR A1067 PHE 0.026 0.002 PHE B 515 TRP 0.014 0.001 TRP B1102 HIS 0.013 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (24198) covalent geometry : angle 0.70151 / 0.36 (32913) SS BOND : bond 0.00629 / 0.40 ( 36) SS BOND : angle 3.26791 / 2.17 ( 72) hydrogen bonds : bond 0.04724 / 3.06 ( 988) hydrogen bonds : angle 5.53296 / 3.83 ( 2748) Misc. bond : bond 0.00261 / 0.12 ( 3) link_BETA1-4 : bond 0.00389 / 0.22 ( 15) link_BETA1-4 : angle 1.27311 / 0.89 ( 45) link_NAG-ASN : bond 0.00644 / 0.42 ( 32) link_NAG-ASN : angle 3.50977 / 2.41 ( 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 619 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 557 time to evaluate : 0.795 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: 0.7428 (tp40) cc_final: 0.7108 (tp40) REVERT: A 237 ARG cc_start: 0.7264 (mtp85) cc_final: 0.7005 (mtp85) REVERT: A 266 TYR cc_start: 0.7965 (m-80) cc_final: 0.7683 (m-80) REVERT: A 281 GLU cc_start: 0.7190 (tp30) cc_final: 0.6783 (tp30) REVERT: A 299 THR cc_start: 0.8432 (m) cc_final: 0.8222 (t) REVERT: A 304 LYS cc_start: 0.8393 (mttp) cc_final: 0.8117 (ttmm) REVERT: A 305 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8330 (p) REVERT: A 307 THR cc_start: 0.8504 (m) cc_final: 0.8202 (t) REVERT: A 395 VAL cc_start: 0.7826 (t) cc_final: 0.7622 (t) REVERT: A 406 GLU cc_start: 0.7407 (pm20) cc_final: 0.7198 (pm20) REVERT: A 429 PHE cc_start: 0.7917 (t80) cc_final: 0.7610 (t80) REVERT: A 578 ASP cc_start: 0.7919 (t0) cc_final: 0.7524 (t0) REVERT: A 745 ASP cc_start: 0.7368 (t70) cc_final: 0.7051 (p0) REVERT: A 759 PHE cc_start: 0.8167 (m-10) cc_final: 0.7965 (m-80) REVERT: A 765 ARG cc_start: 0.8028 (ptm-80) cc_final: 0.7731 (ttm-80) REVERT: A 779 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7801 (tm-30) REVERT: A 918 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: A 933 LYS cc_start: 0.8112 (mttm) cc_final: 0.7696 (mtmm) REVERT: A 949 GLN cc_start: 0.7472 (tp40) cc_final: 0.7164 (tp40) REVERT: A 957 GLN cc_start: 0.8009 (mm110) cc_final: 0.7750 (mm110) REVERT: A 1002 GLN cc_start: 0.8482 (tp40) cc_final: 0.7803 (tm-30) REVERT: A 1050 MET cc_start: 0.8420 (ptp) cc_final: 0.8212 (ptp) REVERT: B 55 PHE cc_start: 0.7634 (m-80) cc_final: 0.7132 (m-80) REVERT: B 115 GLN cc_start: 0.7452 (mp10) cc_final: 0.7156 (mp10) REVERT: B 135 PHE cc_start: 0.4959 (m-80) cc_final: 0.4738 (m-80) REVERT: B 169 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7501 (tm-30) REVERT: B 202 LYS cc_start: 0.7932 (ttpp) cc_final: 0.7708 (ptmt) REVERT: B 237 ARG cc_start: 0.7159 (mtp85) cc_final: 0.6735 (mtp85) REVERT: B 239 GLN cc_start: 0.8233 (tt0) cc_final: 0.7992 (tt0) REVERT: B 276 LEU cc_start: 0.7795 (tt) cc_final: 0.7496 (tp) REVERT: B 281 GLU cc_start: 0.6560 (tp30) cc_final: 0.6138 (tp30) REVERT: B 289 VAL cc_start: 0.7814 (t) cc_final: 0.7404 (m) REVERT: B 290 ASP cc_start: 0.7505 (p0) cc_final: 0.7268 (p0) REVERT: B 307 THR cc_start: 0.8167 (m) cc_final: 0.7833 (p) REVERT: B 357 ARG cc_start: 0.7321 (mpt180) cc_final: 0.6928 (mpt180) REVERT: B 365 TYR cc_start: 0.8003 (m-80) cc_final: 0.7435 (m-80) REVERT: B 382 VAL cc_start: 0.8602 (t) cc_final: 0.8334 (m) REVERT: B 398 ASP cc_start: 0.7998 (m-30) cc_final: 0.7477 (m-30) REVERT: B 554 GLU cc_start: 0.7841 (pm20) cc_final: 0.7615 (pm20) REVERT: B 567 ARG cc_start: 0.8029 (tpp80) cc_final: 0.7543 (ttm-80) REVERT: B 651 ILE cc_start: 0.8686 (mt) cc_final: 0.8431 (mt) REVERT: B 661 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: B 716 THR cc_start: 0.8795 (t) cc_final: 0.8541 (p) REVERT: B 726 ILE cc_start: 0.8595 (mm) cc_final: 0.8251 (mm) REVERT: B 765 ARG cc_start: 0.7888 (ttm110) cc_final: 0.7466 (ttm110) REVERT: B 779 GLN cc_start: 0.8290 (tp40) cc_final: 0.7922 (tp40) REVERT: B 815 ARG cc_start: 0.7903 (ptp-170) cc_final: 0.7686 (ptt180) REVERT: B 872 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7775 (tp40) REVERT: B 904 TYR cc_start: 0.6955 (m-10) cc_final: 0.6554 (m-10) REVERT: B 933 LYS cc_start: 0.8165 (mttt) cc_final: 0.7748 (mmtm) REVERT: B 936 ASP cc_start: 0.7734 (m-30) cc_final: 0.7474 (m-30) REVERT: B 954 GLN cc_start: 0.7582 (mt0) cc_final: 0.7166 (mt0) REVERT: B 977 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8022 (mt) REVERT: B 1000 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8136 (mtt180) REVERT: B 1038 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8589 (mmmm) REVERT: B 1045 LYS cc_start: 0.8199 (ptmm) cc_final: 0.7959 (mtpt) REVERT: B 1107 ARG cc_start: 0.7680 (mtt180) cc_final: 0.7403 (mpt180) REVERT: C 195 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7755 (ptmt) REVERT: C 240 THR cc_start: 0.8309 (m) cc_final: 0.7846 (t) REVERT: C 271 GLN cc_start: 0.7753 (pm20) cc_final: 0.7431 (pm20) REVERT: C 273 ARG cc_start: 0.7974 (ptm160) cc_final: 0.7766 (ptp-170) REVERT: C 278 LYS cc_start: 0.8031 (tttt) cc_final: 0.7741 (ttmt) REVERT: C 305 SER cc_start: 0.8938 (t) cc_final: 0.8677 (m) REVERT: C 308 VAL cc_start: 0.7886 (t) cc_final: 0.7638 (t) REVERT: C 320 VAL cc_start: 0.8694 (t) cc_final: 0.8258 (m) REVERT: C 428 ASP cc_start: 0.7515 (p0) cc_final: 0.7171 (p0) REVERT: C 514 SER cc_start: 0.8368 (t) cc_final: 0.7902 (p) REVERT: C 529 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7976 (mmtt) REVERT: C 551 VAL cc_start: 0.8733 (m) cc_final: 0.8490 (p) REVERT: C 558 LYS cc_start: 0.8418 (mppt) cc_final: 0.8141 (mppt) REVERT: C 610 VAL cc_start: 0.8614 (t) cc_final: 0.8405 (t) REVERT: C 654 GLU cc_start: 0.7748 (tp30) cc_final: 0.7281 (tp30) REVERT: C 736 VAL cc_start: 0.8413 (m) cc_final: 0.8153 (t) REVERT: C 779 GLN cc_start: 0.8511 (tp40) cc_final: 0.7961 (tm-30) REVERT: C 914 ASN cc_start: 0.8113 (m-40) cc_final: 0.7765 (m110) REVERT: C 931 ILE cc_start: 0.7877 (mm) cc_final: 0.7570 (mm) REVERT: C 950 ASP cc_start: 0.7320 (t0) cc_final: 0.6983 (t0) REVERT: C 954 GLN cc_start: 0.7483 (mt0) cc_final: 0.7186 (mt0) REVERT: C 988 GLU cc_start: 0.8102 (pm20) cc_final: 0.7885 (mp0) REVERT: C 1005 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7829 (mm-40) REVERT: C 1133 VAL cc_start: 0.8773 (p) cc_final: 0.8380 (m) outliers start: 62 outliers final: 40 residues processed: 596 average time/residue: 0.1707 time to fit residues: 155.8864 Evaluate side-chains 574 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 527 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 305 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 918 GLU 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 197 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 730 SER 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 977 LEU Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1107 ARG 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: 0.6980 chunk 273 optimal weight: 0.6980 chunk 226 optimal weight: 0.9980 chunk 251 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 206 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 151 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 784 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 ASN B1048 HIS ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.158909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.125598 restraints weight = 35835.489| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.06 r_work: 0.3351 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 1.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24284 Z= 0.195 Angle : 0.751 20.504 33126 Z= 0.381 Chirality : 0.048 0.373 3932 Planarity : 0.005 0.063 4164 Dihedral : 4.840 36.378 3099 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.23 % Allowed : 23.04 % Favored : 74.73 % 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: -0.29 (0.15), residues: 2844 helix: 1.31 (0.20), residues: 738 sheet: -0.23 (0.19), residues: 702 loop : -0.96 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 237 TYR 0.026 0.002 TYR A1067 PHE 0.026 0.002 PHE B 515 TRP 0.016 0.002 TRP A1102 HIS 0.010 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (24198) covalent geometry : angle 0.71265 / 0.37 (32913) SS BOND : bond 0.00672 / 0.44 ( 36) SS BOND : angle 3.19134 / 2.08 ( 72) hydrogen bonds : bond 0.04746 / 3.04 ( 988) hydrogen bonds : angle 5.52067 / 3.81 ( 2748) Misc. bond : bond 0.00165 / 0.08 ( 3) link_BETA1-4 : bond 0.00380 / 0.20 ( 15) link_BETA1-4 : angle 1.30240 / 0.92 ( 45) link_NAG-ASN : bond 0.00627 / 0.41 ( 32) link_NAG-ASN : angle 3.50609 / 2.41 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5506.97 seconds wall clock time: 95 minutes 30.32 seconds (5730.32 seconds total)