Starting phenix.real_space_refine on Thu Mar 5 12:18:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x79_22083/03_2026/6x79_22083.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x79_22083/03_2026/6x79_22083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x79_22083/03_2026/6x79_22083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x79_22083/03_2026/6x79_22083.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x79_22083/03_2026/6x79_22083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x79_22083/03_2026/6x79_22083.map" } resolution = 2.9 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= 0.004 sd= 0.106 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 102 5.16 5 C 14187 2.51 5 N 3660 2.21 5 O 4302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22251 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 950, 7179 Classifications: {'peptide': 950} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 45, 'TRANS': 904} Chain breaks: 14 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 6, 'GLU:plan': 6, 'GLN:plan1': 5, 'PHE:plan': 3, 'ARG:plan': 3, 'HIS:plan': 2, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 186 Chain: "B" Number of atoms: 7179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 950, 7179 Classifications: {'peptide': 950} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 45, 'TRANS': 904} Chain breaks: 14 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 6, 'GLU:plan': 6, 'GLN:plan1': 5, 'PHE:plan': 3, 'ARG:plan': 3, 'HIS:plan': 2, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 186 Chain: "C" Number of atoms: 7179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 950, 7179 Classifications: {'peptide': 950} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 45, 'TRANS': 904} Chain breaks: 14 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 6, 'GLU:plan': 6, 'GLN:plan1': 5, 'PHE:plan': 3, 'ARG:plan': 3, 'HIS:plan': 2, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 186 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.59, per 1000 atoms: 0.25 Number of scatterers: 22251 At special positions: 0 Unit cell: (128.76, 128.76, 162.4, 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 102 16.00 O 4302 8.00 N 3660 7.00 C 14187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS C 383 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 985 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 603 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 603 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 603 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN B 234 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN C 234 " " NAG K 1 " - " ASN C 717 " " NAG L 1 " - " ASN C 801 " Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 967.4 milliseconds 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5352 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 25.5% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.465A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.371A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.112A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.805A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.512A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.634A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.947A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.302A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.465A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.371A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.112A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.805A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.512A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.635A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.948A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.454A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.466A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.371A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.113A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.805A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.512A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.635A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.948A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.298A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.382A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.486A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.280A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.329A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.172A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.172A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.819A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 453 removed outlier: 5.829A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.139A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.933A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.461A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.461A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.854A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.381A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.854A 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 55 removed outlier: 7.487A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.280A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.329A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.171A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.171A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.820A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 448 through 453 removed outlier: 5.829A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.139A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.934A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.461A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.461A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.394A 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: 4.853A 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: 8.382A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.854A 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: 7.486A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.279A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.329A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.172A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.172A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.820A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 448 through 453 removed outlier: 5.829A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.140A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.460A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.460A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.853A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1006 hydrogen bonds defined for protein. 2802 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: 5.24 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3922 1.32 - 1.45: 6780 1.45 - 1.59: 11860 1.59 - 1.72: 7 1.72 - 1.86: 126 Bond restraints: 22695 Sorted by residual: bond pdb=" NE ARG C 454 " pdb=" CZ ARG C 454 " ideal model delta sigma weight residual 1.326 1.383 -0.057 1.10e-02 8.26e+03 2.66e+01 bond pdb=" NE ARG B 454 " pdb=" CZ ARG B 454 " ideal model delta sigma weight residual 1.326 1.382 -0.056 1.10e-02 8.26e+03 2.62e+01 bond pdb=" NE ARG A 454 " pdb=" CZ ARG A 454 " ideal model delta sigma weight residual 1.326 1.382 -0.056 1.10e-02 8.26e+03 2.60e+01 bond pdb=" C ALA A 989 " pdb=" O ALA A 989 " ideal model delta sigma weight residual 1.236 1.183 0.053 1.15e-02 7.56e+03 2.13e+01 bond pdb=" CA ALA B 989 " pdb=" C ALA B 989 " ideal model delta sigma weight residual 1.524 1.464 0.060 1.32e-02 5.74e+03 2.05e+01 ... (remaining 22690 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 25653 1.65 - 3.31: 4354 3.31 - 4.96: 603 4.96 - 6.61: 250 6.61 - 8.27: 43 Bond angle restraints: 30903 Sorted by residual: angle pdb=" C PRO B 862 " pdb=" N PRO B 863 " pdb=" CA PRO B 863 " ideal model delta sigma weight residual 120.03 127.41 -7.38 9.90e-01 1.02e+00 5.56e+01 angle pdb=" C PRO A 862 " pdb=" N PRO A 863 " pdb=" CA PRO A 863 " ideal model delta sigma weight residual 120.03 127.41 -7.38 9.90e-01 1.02e+00 5.56e+01 angle pdb=" C PRO C 862 " pdb=" N PRO C 863 " pdb=" CA PRO C 863 " ideal model delta sigma weight residual 120.03 127.37 -7.34 9.90e-01 1.02e+00 5.50e+01 angle pdb=" C GLN A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.56 126.89 -7.33 1.02e+00 9.61e-01 5.16e+01 angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.56 126.87 -7.31 1.02e+00 9.61e-01 5.13e+01 ... (remaining 30898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 13550 17.69 - 35.38: 446 35.38 - 53.07: 77 53.07 - 70.76: 66 70.76 - 88.45: 15 Dihedral angle restraints: 14154 sinusoidal: 5892 harmonic: 8262 Sorted by residual: dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual -86.00 -160.35 74.35 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -160.35 74.35 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -160.35 74.35 1 1.00e+01 1.00e-02 7.01e+01 ... (remaining 14151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2733 0.084 - 0.168: 759 0.168 - 0.252: 162 0.252 - 0.336: 68 0.336 - 0.420: 46 Chirality restraints: 3768 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.54e+01 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.46e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.34e+01 ... (remaining 3765 not shown) Planarity restraints: 3948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.051 2.00e-02 2.50e+03 5.19e-02 3.37e+01 pdb=" CG ASN B 331 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.077 2.00e-02 2.50e+03 pdb=" C1 NAG B1303 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.051 2.00e-02 2.50e+03 5.18e-02 3.36e+01 pdb=" CG ASN A 331 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.077 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.051 2.00e-02 2.50e+03 5.16e-02 3.33e+01 pdb=" CG ASN C 331 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.077 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " 0.063 2.00e-02 2.50e+03 ... (remaining 3945 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 7957 2.89 - 3.39: 19584 3.39 - 3.89: 36598 3.89 - 4.40: 41744 4.40 - 4.90: 70192 Nonbonded interactions: 176075 Sorted by model distance: nonbonded pdb=" NZ LYS C 811 " pdb=" OD2 ASP C 820 " model vdw 2.382 3.120 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.382 3.120 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.383 3.120 nonbonded pdb=" N PRO C 600 " pdb=" O PRO C 600 " model vdw 2.495 2.496 nonbonded pdb=" N PRO B 600 " pdb=" O PRO B 600 " model vdw 2.495 2.496 ... (remaining 176070 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: 0.04 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' } 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: 4.010 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: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.340 Find NCS groups from input model: 0.400 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:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 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 : 0.014 0.088 22785 Z= 0.742 Angle : 1.373 10.181 31134 Z= 0.907 Chirality : 0.096 0.420 3768 Planarity : 0.005 0.042 3906 Dihedral : 10.282 88.451 8685 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 0.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.26 % Allowed : 0.39 % Favored : 99.35 % 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: 0.59 (0.14), residues: 2760 helix: 0.27 (0.18), residues: 654 sheet: 1.47 (0.19), residues: 603 loop : 0.09 (0.14), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1000 TYR 0.027 0.004 TYR B 170 PHE 0.018 0.003 PHE A 58 TRP 0.032 0.006 TRP B 886 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.01372 (22695) covalent geometry : angle 1.34636 (30903) SS BOND : bond 0.01009 ( 39) SS BOND : angle 4.64275 ( 78) hydrogen bonds : bond 0.18023 ( 973) hydrogen bonds : angle 7.88903 ( 2802) link_BETA1-4 : bond 0.06457 ( 9) link_BETA1-4 : angle 3.66143 ( 27) link_NAG-ASN : bond 0.06728 ( 42) link_NAG-ASN : angle 2.19903 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 484 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 306 PHE cc_start: 0.7828 (m-10) cc_final: 0.7606 (m-80) REVERT: A 787 GLN cc_start: 0.6897 (mt0) cc_final: 0.6660 (mt0) REVERT: A 856 ASN cc_start: 0.7091 (m-40) cc_final: 0.6867 (m-40) REVERT: B 523 THR cc_start: 0.7236 (p) cc_final: 0.6922 (t) REVERT: B 773 GLU cc_start: 0.7178 (tt0) cc_final: 0.6886 (tt0) REVERT: B 786 LYS cc_start: 0.7222 (mtmm) cc_final: 0.7000 (mmtt) REVERT: B 856 ASN cc_start: 0.7135 (m-40) cc_final: 0.6902 (m-40) REVERT: C 731 MET cc_start: 0.8803 (ptm) cc_final: 0.8483 (ptm) REVERT: C 856 ASN cc_start: 0.6953 (m-40) cc_final: 0.6729 (m110) outliers start: 6 outliers final: 4 residues processed: 490 average time/residue: 0.5558 time to fit residues: 314.6107 Evaluate side-chains 254 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 250 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 985 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 675 GLN A 935 GLN A1010 GLN A1113 GLN A1119 ASN B 207 HIS B 580 GLN B 675 GLN B 919 ASN B 935 GLN B 965 GLN B1113 GLN B1119 ASN C 580 GLN C 675 GLN C 762 GLN C 804 GLN C 919 ASN C 935 GLN C 954 GLN C 965 GLN C 978 ASN C1010 GLN C1113 GLN C1119 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.205597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.160957 restraints weight = 26375.209| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.62 r_work: 0.3645 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22785 Z= 0.153 Angle : 0.659 16.993 31134 Z= 0.340 Chirality : 0.047 0.224 3768 Planarity : 0.004 0.040 3906 Dihedral : 6.088 57.862 4071 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.57 % Allowed : 9.41 % Favored : 88.02 % 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: 0.76 (0.15), residues: 2760 helix: 1.31 (0.20), residues: 651 sheet: 1.02 (0.18), residues: 690 loop : -0.08 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1039 TYR 0.021 0.001 TYR A1067 PHE 0.027 0.002 PHE B 92 TRP 0.017 0.002 TRP A 353 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00344 (22695) covalent geometry : angle 0.60402 (30903) SS BOND : bond 0.00375 ( 39) SS BOND : angle 2.26552 ( 78) hydrogen bonds : bond 0.06002 ( 973) hydrogen bonds : angle 6.16968 ( 2802) link_BETA1-4 : bond 0.00446 ( 9) link_BETA1-4 : angle 1.81145 ( 27) link_NAG-ASN : bond 0.00493 ( 42) link_NAG-ASN : angle 3.73377 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 286 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 28 TYR cc_start: 0.5937 (m-80) cc_final: 0.5704 (m-10) REVERT: A 61 ASN cc_start: 0.4784 (m-40) cc_final: 0.3947 (p0) REVERT: A 195 LYS cc_start: 0.8211 (ptpp) cc_final: 0.7987 (ptpp) REVERT: A 357 ARG cc_start: 0.8028 (ptm160) cc_final: 0.7753 (ttp80) REVERT: A 513 LEU cc_start: 0.7531 (mt) cc_final: 0.7297 (mt) REVERT: A 558 LYS cc_start: 0.7973 (ttpp) cc_final: 0.7273 (mptt) REVERT: A 591 SER cc_start: 0.7854 (OUTLIER) cc_final: 0.7362 (m) REVERT: A 645 THR cc_start: 0.7545 (p) cc_final: 0.7048 (t) REVERT: A 780 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7862 (pt0) REVERT: A 856 ASN cc_start: 0.8118 (m-40) cc_final: 0.7798 (m-40) REVERT: A 918 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: A 995 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7688 (mmm-85) REVERT: A 1138 TYR cc_start: 0.6923 (t80) cc_final: 0.6163 (m-10) REVERT: B 319 ARG cc_start: 0.7532 (ttm110) cc_final: 0.6358 (tpt170) REVERT: B 353 TRP cc_start: 0.8727 (p-90) cc_final: 0.8096 (p-90) REVERT: B 368 LEU cc_start: 0.7269 (mp) cc_final: 0.6932 (mp) REVERT: B 523 THR cc_start: 0.7512 (p) cc_final: 0.6860 (t) REVERT: B 773 GLU cc_start: 0.7754 (tt0) cc_final: 0.7420 (tt0) REVERT: B 786 LYS cc_start: 0.7613 (mtmm) cc_final: 0.6912 (mmtt) REVERT: B 983 ARG cc_start: 0.7855 (mtp180) cc_final: 0.7515 (mtp85) REVERT: B 1010 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7666 (pt0) REVERT: B 1138 TYR cc_start: 0.7117 (t80) cc_final: 0.6365 (m-10) REVERT: C 28 TYR cc_start: 0.6054 (m-10) cc_final: 0.5780 (m-10) REVERT: C 303 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6870 (mt) REVERT: C 319 ARG cc_start: 0.7299 (ttm110) cc_final: 0.7098 (mtp-110) REVERT: C 428 ASP cc_start: 0.7736 (p0) cc_final: 0.7459 (p0) REVERT: C 567 ARG cc_start: 0.6915 (mtt90) cc_final: 0.6254 (mpt180) REVERT: C 612 TYR cc_start: 0.8574 (m-80) cc_final: 0.8302 (m-80) REVERT: C 645 THR cc_start: 0.7342 (p) cc_final: 0.7083 (t) REVERT: C 731 MET cc_start: 0.8967 (ptm) cc_final: 0.8585 (ptm) REVERT: C 804 GLN cc_start: 0.8113 (mt0) cc_final: 0.7881 (mp10) REVERT: C 979 ASP cc_start: 0.8429 (m-30) cc_final: 0.8223 (m-30) REVERT: C 1119 ASN cc_start: 0.7664 (m-40) cc_final: 0.7216 (m110) REVERT: C 1138 TYR cc_start: 0.7012 (t80) cc_final: 0.6331 (m-10) outliers start: 59 outliers final: 24 residues processed: 326 average time/residue: 0.5398 time to fit residues: 204.8228 Evaluate side-chains 245 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 985 CYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 142 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 chunk 3 optimal weight: 0.0000 chunk 263 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 201 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 273 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 207 HIS A 935 GLN A 955 ASN A 965 GLN A1010 GLN A1119 ASN B 644 GLN B 675 GLN B 955 ASN B1071 GLN B1101 HIS C 87 ASN C 544 ASN C 644 GLN C 675 GLN C1010 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.203889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.150055 restraints weight = 26272.113| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.17 r_work: 0.3605 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22785 Z= 0.134 Angle : 0.569 16.548 31134 Z= 0.292 Chirality : 0.045 0.187 3768 Planarity : 0.004 0.041 3906 Dihedral : 5.212 49.229 4071 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.49 % Allowed : 10.63 % Favored : 85.88 % 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: 0.68 (0.15), residues: 2760 helix: 1.49 (0.20), residues: 675 sheet: 0.79 (0.18), residues: 702 loop : -0.18 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 567 TYR 0.020 0.001 TYR A1067 PHE 0.023 0.002 PHE B 55 TRP 0.014 0.002 TRP A 353 HIS 0.005 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00305 (22695) covalent geometry : angle 0.51814 (30903) SS BOND : bond 0.00425 ( 39) SS BOND : angle 1.79841 ( 78) hydrogen bonds : bond 0.05208 ( 973) hydrogen bonds : angle 5.75182 ( 2802) link_BETA1-4 : bond 0.00486 ( 9) link_BETA1-4 : angle 1.34942 ( 27) link_NAG-ASN : bond 0.00709 ( 42) link_NAG-ASN : angle 3.44320 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 254 time to evaluate : 0.677 Fit side-chains REVERT: A 40 ASP cc_start: 0.6797 (OUTLIER) cc_final: 0.6564 (m-30) REVERT: A 50 SER cc_start: 0.8490 (t) cc_final: 0.8138 (t) REVERT: A 61 ASN cc_start: 0.4805 (m-40) cc_final: 0.4030 (p0) REVERT: A 195 LYS cc_start: 0.8181 (ptpp) cc_final: 0.7911 (ptpp) REVERT: A 357 ARG cc_start: 0.8023 (ptm160) cc_final: 0.7763 (ttp80) REVERT: A 513 LEU cc_start: 0.7795 (mt) cc_final: 0.7412 (mt) REVERT: A 558 LYS cc_start: 0.8178 (ttpp) cc_final: 0.7413 (mptt) REVERT: A 576 VAL cc_start: 0.8789 (t) cc_final: 0.8379 (p) REVERT: A 645 THR cc_start: 0.7513 (p) cc_final: 0.6828 (t) REVERT: A 787 GLN cc_start: 0.7854 (mt0) cc_final: 0.7429 (mt0) REVERT: A 918 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: A 1138 TYR cc_start: 0.7044 (t80) cc_final: 0.6257 (m-10) REVERT: B 40 ASP cc_start: 0.6511 (OUTLIER) cc_final: 0.5906 (p0) REVERT: B 353 TRP cc_start: 0.8693 (p-90) cc_final: 0.8154 (p-90) REVERT: B 584 ILE cc_start: 0.6802 (OUTLIER) cc_final: 0.6032 (mm) REVERT: B 786 LYS cc_start: 0.7735 (mtmm) cc_final: 0.7099 (mmtt) REVERT: B 983 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7616 (mtp85) REVERT: B 995 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7256 (mpp80) REVERT: B 1010 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7669 (pt0) REVERT: B 1138 TYR cc_start: 0.7072 (t80) cc_final: 0.6325 (m-10) REVERT: C 28 TYR cc_start: 0.5968 (m-10) cc_final: 0.5737 (m-10) REVERT: C 195 LYS cc_start: 0.8167 (ptpp) cc_final: 0.7842 (ptpp) REVERT: C 303 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6829 (mt) REVERT: C 368 LEU cc_start: 0.7202 (mp) cc_final: 0.6830 (mp) REVERT: C 428 ASP cc_start: 0.7724 (p0) cc_final: 0.7427 (p0) REVERT: C 567 ARG cc_start: 0.7039 (mtt90) cc_final: 0.6325 (mpt180) REVERT: C 612 TYR cc_start: 0.8666 (m-80) cc_final: 0.8389 (m-80) REVERT: C 645 THR cc_start: 0.7374 (p) cc_final: 0.6774 (t) REVERT: C 731 MET cc_start: 0.9018 (ptm) cc_final: 0.8653 (ptm) REVERT: C 790 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8383 (mtmt) REVERT: C 856 ASN cc_start: 0.7973 (m-40) cc_final: 0.7503 (m-40) REVERT: C 979 ASP cc_start: 0.8443 (m-30) cc_final: 0.8186 (m-30) REVERT: C 983 ARG cc_start: 0.7940 (mtm110) cc_final: 0.7716 (mtm110) REVERT: C 1114 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7989 (tp) REVERT: C 1138 TYR cc_start: 0.6945 (t80) cc_final: 0.6481 (m-10) outliers start: 80 outliers final: 30 residues processed: 310 average time/residue: 0.5043 time to fit residues: 183.8273 Evaluate side-chains 260 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 985 CYS Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 173 optimal weight: 0.0060 chunk 9 optimal weight: 0.3980 chunk 190 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A1010 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 675 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.203930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.158614 restraints weight = 26316.544| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.60 r_work: 0.3595 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22785 Z= 0.116 Angle : 0.538 16.801 31134 Z= 0.273 Chirality : 0.044 0.164 3768 Planarity : 0.004 0.032 3906 Dihedral : 4.820 50.221 4071 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.31 % Allowed : 11.90 % Favored : 84.79 % 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: 0.71 (0.15), residues: 2760 helix: 1.67 (0.21), residues: 675 sheet: 0.77 (0.19), residues: 690 loop : -0.23 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 319 TYR 0.019 0.001 TYR A1067 PHE 0.020 0.001 PHE B 92 TRP 0.014 0.002 TRP A 353 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00266 (22695) covalent geometry : angle 0.49212 (30903) SS BOND : bond 0.00234 ( 39) SS BOND : angle 1.65545 ( 78) hydrogen bonds : bond 0.04570 ( 973) hydrogen bonds : angle 5.48409 ( 2802) link_BETA1-4 : bond 0.00341 ( 9) link_BETA1-4 : angle 1.30006 ( 27) link_NAG-ASN : bond 0.00523 ( 42) link_NAG-ASN : angle 3.15854 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 244 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6922 (OUTLIER) cc_final: 0.6247 (p0) REVERT: A 50 SER cc_start: 0.8400 (t) cc_final: 0.8183 (t) REVERT: A 61 ASN cc_start: 0.4921 (m-40) cc_final: 0.3992 (p0) REVERT: A 319 ARG cc_start: 0.7223 (ttm110) cc_final: 0.6142 (tpt170) REVERT: A 357 ARG cc_start: 0.8153 (ptm160) cc_final: 0.7725 (ttp-170) REVERT: A 368 LEU cc_start: 0.7024 (mp) cc_final: 0.6641 (mp) REVERT: A 513 LEU cc_start: 0.7780 (mt) cc_final: 0.7485 (mt) REVERT: A 576 VAL cc_start: 0.8748 (t) cc_final: 0.8418 (p) REVERT: A 645 THR cc_start: 0.7513 (p) cc_final: 0.6997 (t) REVERT: A 787 GLN cc_start: 0.7899 (mt0) cc_final: 0.7468 (mt0) REVERT: A 918 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: A 1038 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8466 (mptt) REVERT: A 1138 TYR cc_start: 0.7066 (t80) cc_final: 0.6288 (m-10) REVERT: B 40 ASP cc_start: 0.6488 (OUTLIER) cc_final: 0.5942 (p0) REVERT: B 319 ARG cc_start: 0.7537 (ttm110) cc_final: 0.6222 (tpt170) REVERT: B 353 TRP cc_start: 0.8704 (p-90) cc_final: 0.8226 (p-90) REVERT: B 360 ASN cc_start: 0.7459 (t0) cc_final: 0.6530 (t0) REVERT: B 513 LEU cc_start: 0.7686 (mt) cc_final: 0.7325 (mt) REVERT: B 645 THR cc_start: 0.7563 (OUTLIER) cc_final: 0.7159 (t) REVERT: B 786 LYS cc_start: 0.7839 (mtmm) cc_final: 0.7186 (mmtt) REVERT: B 886 TRP cc_start: 0.7596 (p90) cc_final: 0.7256 (p90) REVERT: B 983 ARG cc_start: 0.7943 (mtp180) cc_final: 0.7584 (mtp85) REVERT: B 995 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7278 (mpp80) REVERT: B 1010 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: B 1138 TYR cc_start: 0.7133 (t80) cc_final: 0.6386 (m-10) REVERT: C 195 LYS cc_start: 0.8056 (ptpp) cc_final: 0.7802 (mtpt) REVERT: C 303 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6715 (mt) REVERT: C 319 ARG cc_start: 0.7459 (ttm110) cc_final: 0.6047 (tpt170) REVERT: C 360 ASN cc_start: 0.7680 (t0) cc_final: 0.6989 (p0) REVERT: C 428 ASP cc_start: 0.7675 (p0) cc_final: 0.7364 (p0) REVERT: C 513 LEU cc_start: 0.7952 (mt) cc_final: 0.7620 (mt) REVERT: C 584 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6180 (mm) REVERT: C 612 TYR cc_start: 0.8619 (m-80) cc_final: 0.8359 (m-80) REVERT: C 645 THR cc_start: 0.7426 (p) cc_final: 0.7052 (t) REVERT: C 731 MET cc_start: 0.9022 (ptm) cc_final: 0.8606 (ptm) REVERT: C 979 ASP cc_start: 0.8477 (m-30) cc_final: 0.8240 (m-30) REVERT: C 1138 TYR cc_start: 0.7028 (t80) cc_final: 0.6585 (m-10) outliers start: 76 outliers final: 34 residues processed: 299 average time/residue: 0.4652 time to fit residues: 166.0008 Evaluate side-chains 263 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 985 CYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 0.8980 chunk 229 optimal weight: 0.2980 chunk 173 optimal weight: 0.6980 chunk 209 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 280 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 246 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A 965 GLN A1010 GLN A1071 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 675 GLN C1010 GLN C1071 GLN C1119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.202693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.148438 restraints weight = 26043.116| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.15 r_work: 0.3611 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22785 Z= 0.133 Angle : 0.541 16.522 31134 Z= 0.274 Chirality : 0.044 0.157 3768 Planarity : 0.004 0.032 3906 Dihedral : 4.586 49.613 4069 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.53 % Allowed : 12.42 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.15), residues: 2760 helix: 1.70 (0.21), residues: 675 sheet: 0.71 (0.19), residues: 690 loop : -0.32 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 319 TYR 0.019 0.001 TYR A1067 PHE 0.024 0.001 PHE B 55 TRP 0.017 0.002 TRP A 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00313 (22695) covalent geometry : angle 0.49700 (30903) SS BOND : bond 0.00310 ( 39) SS BOND : angle 1.71066 ( 78) hydrogen bonds : bond 0.04780 ( 973) hydrogen bonds : angle 5.43989 ( 2802) link_BETA1-4 : bond 0.00353 ( 9) link_BETA1-4 : angle 1.26237 ( 27) link_NAG-ASN : bond 0.00506 ( 42) link_NAG-ASN : angle 3.10410 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 228 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6266 (p0) REVERT: A 50 SER cc_start: 0.8407 (t) cc_final: 0.8175 (t) REVERT: A 61 ASN cc_start: 0.5012 (m-40) cc_final: 0.4079 (p0) REVERT: A 319 ARG cc_start: 0.7090 (ttm110) cc_final: 0.6064 (tpt170) REVERT: A 357 ARG cc_start: 0.8156 (ptm160) cc_final: 0.7722 (ttp-170) REVERT: A 513 LEU cc_start: 0.7799 (mt) cc_final: 0.7481 (mt) REVERT: A 576 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8436 (p) REVERT: A 645 THR cc_start: 0.7509 (p) cc_final: 0.6944 (t) REVERT: A 787 GLN cc_start: 0.7970 (mt0) cc_final: 0.7541 (mt0) REVERT: A 918 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: A 1138 TYR cc_start: 0.7031 (t80) cc_final: 0.6310 (m-10) REVERT: B 40 ASP cc_start: 0.6463 (OUTLIER) cc_final: 0.5979 (p0) REVERT: B 353 TRP cc_start: 0.8663 (p-90) cc_final: 0.8127 (p-90) REVERT: B 360 ASN cc_start: 0.7492 (t0) cc_final: 0.6561 (t0) REVERT: B 513 LEU cc_start: 0.7757 (mt) cc_final: 0.7485 (mt) REVERT: B 584 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6117 (mm) REVERT: B 645 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7245 (t) REVERT: B 786 LYS cc_start: 0.7872 (mtmm) cc_final: 0.7238 (mmtt) REVERT: B 983 ARG cc_start: 0.7969 (mtp180) cc_final: 0.7641 (mtp85) REVERT: B 995 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7146 (mpp80) REVERT: B 1010 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7729 (pt0) REVERT: B 1138 TYR cc_start: 0.7185 (t80) cc_final: 0.6483 (m-10) REVERT: C 195 LYS cc_start: 0.8063 (ptpp) cc_final: 0.7830 (mtpt) REVERT: C 303 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6837 (mt) REVERT: C 360 ASN cc_start: 0.7674 (t0) cc_final: 0.6961 (p0) REVERT: C 428 ASP cc_start: 0.7713 (p0) cc_final: 0.7381 (p0) REVERT: C 513 LEU cc_start: 0.7946 (mt) cc_final: 0.7560 (mt) REVERT: C 584 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6179 (mm) REVERT: C 612 TYR cc_start: 0.8655 (m-80) cc_final: 0.8390 (m-80) REVERT: C 731 MET cc_start: 0.9064 (ptm) cc_final: 0.8642 (ptm) REVERT: C 784 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7527 (mt0) outliers start: 81 outliers final: 40 residues processed: 285 average time/residue: 0.4549 time to fit residues: 156.0405 Evaluate side-chains 268 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 217 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 93 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 265 optimal weight: 2.9990 chunk 162 optimal weight: 0.0270 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 182 optimal weight: 0.9980 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN A1010 GLN A1135 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 675 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.198884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.154060 restraints weight = 26306.322| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.62 r_work: 0.3528 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 22785 Z= 0.213 Angle : 0.619 15.814 31134 Z= 0.313 Chirality : 0.047 0.166 3768 Planarity : 0.004 0.034 3906 Dihedral : 4.845 45.713 4068 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.66 % Allowed : 13.29 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 2760 helix: 1.37 (0.20), residues: 675 sheet: 0.51 (0.19), residues: 690 loop : -0.52 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 319 TYR 0.021 0.002 TYR A1067 PHE 0.022 0.002 PHE B 92 TRP 0.013 0.002 TRP A 353 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00522 (22695) covalent geometry : angle 0.57687 (30903) SS BOND : bond 0.00463 ( 39) SS BOND : angle 2.20935 ( 78) hydrogen bonds : bond 0.05865 ( 973) hydrogen bonds : angle 5.67624 ( 2802) link_BETA1-4 : bond 0.00325 ( 9) link_BETA1-4 : angle 1.34981 ( 27) link_NAG-ASN : bond 0.00469 ( 42) link_NAG-ASN : angle 3.10816 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 234 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6831 (OUTLIER) cc_final: 0.6153 (p0) REVERT: A 50 SER cc_start: 0.8427 (t) cc_final: 0.8187 (t) REVERT: A 61 ASN cc_start: 0.5018 (m-40) cc_final: 0.4095 (p0) REVERT: A 558 LYS cc_start: 0.8142 (ttpp) cc_final: 0.7408 (mptt) REVERT: A 576 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8436 (p) REVERT: A 584 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7167 (mm) REVERT: A 787 GLN cc_start: 0.8030 (mt0) cc_final: 0.7578 (mt0) REVERT: A 918 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: A 950 ASP cc_start: 0.8463 (m-30) cc_final: 0.8084 (m-30) REVERT: A 979 ASP cc_start: 0.8356 (m-30) cc_final: 0.8151 (m-30) REVERT: A 1138 TYR cc_start: 0.7131 (t80) cc_final: 0.6514 (m-10) REVERT: B 40 ASP cc_start: 0.6592 (OUTLIER) cc_final: 0.6377 (m-30) REVERT: B 195 LYS cc_start: 0.8425 (ptpp) cc_final: 0.8131 (ptpp) REVERT: B 353 TRP cc_start: 0.8772 (p-90) cc_final: 0.8057 (p-90) REVERT: B 360 ASN cc_start: 0.7567 (t0) cc_final: 0.6604 (t0) REVERT: B 584 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6094 (mm) REVERT: B 725 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: B 786 LYS cc_start: 0.7881 (mtmm) cc_final: 0.7301 (mmtt) REVERT: B 886 TRP cc_start: 0.7644 (p90) cc_final: 0.7281 (p90) REVERT: B 983 ARG cc_start: 0.7986 (mtp180) cc_final: 0.7680 (mtp85) REVERT: B 995 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7372 (mpp80) REVERT: B 1010 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7750 (pt0) REVERT: B 1138 TYR cc_start: 0.7226 (t80) cc_final: 0.6595 (m-10) REVERT: C 303 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6970 (mt) REVERT: C 360 ASN cc_start: 0.7809 (t0) cc_final: 0.7091 (p0) REVERT: C 403 ARG cc_start: 0.6606 (ttp-170) cc_final: 0.5495 (mpt180) REVERT: C 428 ASP cc_start: 0.7658 (p0) cc_final: 0.7344 (p0) REVERT: C 513 LEU cc_start: 0.7929 (mt) cc_final: 0.7567 (mt) REVERT: C 584 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.6429 (mm) REVERT: C 612 TYR cc_start: 0.8680 (m-80) cc_final: 0.8428 (m-80) REVERT: C 731 MET cc_start: 0.9050 (ptm) cc_final: 0.8732 (ptm) REVERT: C 784 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7588 (mt0) REVERT: C 1138 TYR cc_start: 0.7105 (t80) cc_final: 0.6631 (m-80) outliers start: 84 outliers final: 49 residues processed: 294 average time/residue: 0.4858 time to fit residues: 170.8751 Evaluate side-chains 286 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 225 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 146 optimal weight: 0.0050 chunk 1 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 121 optimal weight: 0.5980 chunk 189 optimal weight: 3.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 675 GLN C1010 GLN C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.200732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.155319 restraints weight = 26028.963| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.58 r_work: 0.3557 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22785 Z= 0.135 Angle : 0.551 15.039 31134 Z= 0.276 Chirality : 0.045 0.166 3768 Planarity : 0.004 0.042 3906 Dihedral : 4.713 47.799 4068 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.27 % Allowed : 14.42 % Favored : 82.31 % 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: 0.40 (0.15), residues: 2760 helix: 1.53 (0.21), residues: 675 sheet: 0.53 (0.19), residues: 678 loop : -0.46 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 357 TYR 0.020 0.001 TYR C1138 PHE 0.028 0.001 PHE B 55 TRP 0.023 0.002 TRP A 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00320 (22695) covalent geometry : angle 0.51090 (30903) SS BOND : bond 0.00277 ( 39) SS BOND : angle 1.88893 ( 78) hydrogen bonds : bond 0.04893 ( 973) hydrogen bonds : angle 5.48426 ( 2802) link_BETA1-4 : bond 0.00307 ( 9) link_BETA1-4 : angle 1.26734 ( 27) link_NAG-ASN : bond 0.00428 ( 42) link_NAG-ASN : angle 2.88891 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 236 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6138 (p0) REVERT: A 50 SER cc_start: 0.8440 (t) cc_final: 0.8188 (t) REVERT: A 61 ASN cc_start: 0.5015 (m-40) cc_final: 0.4058 (p0) REVERT: A 319 ARG cc_start: 0.7076 (ttm110) cc_final: 0.6040 (tpt170) REVERT: A 360 ASN cc_start: 0.7433 (t0) cc_final: 0.6842 (p0) REVERT: A 513 LEU cc_start: 0.7879 (mt) cc_final: 0.7577 (mt) REVERT: A 558 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7431 (mptt) REVERT: A 576 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8432 (p) REVERT: A 787 GLN cc_start: 0.7986 (mt0) cc_final: 0.7545 (mt0) REVERT: A 918 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: A 979 ASP cc_start: 0.8380 (m-30) cc_final: 0.8176 (m-30) REVERT: A 1138 TYR cc_start: 0.7094 (t80) cc_final: 0.6487 (m-10) REVERT: B 40 ASP cc_start: 0.6502 (OUTLIER) cc_final: 0.6001 (p0) REVERT: B 353 TRP cc_start: 0.8693 (p-90) cc_final: 0.8369 (p-90) REVERT: B 360 ASN cc_start: 0.7541 (t0) cc_final: 0.6582 (t0) REVERT: B 403 ARG cc_start: 0.6520 (ttp-170) cc_final: 0.5427 (mpt180) REVERT: B 513 LEU cc_start: 0.7830 (mt) cc_final: 0.7524 (mt) REVERT: B 584 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6091 (mm) REVERT: B 786 LYS cc_start: 0.8039 (mtmm) cc_final: 0.7320 (mmtt) REVERT: B 886 TRP cc_start: 0.7617 (p90) cc_final: 0.7277 (p90) REVERT: B 983 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7625 (mtp85) REVERT: B 995 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7261 (mpp80) REVERT: B 1010 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7729 (pt0) REVERT: B 1138 TYR cc_start: 0.7195 (t80) cc_final: 0.6559 (m-10) REVERT: C 40 ASP cc_start: 0.6434 (OUTLIER) cc_final: 0.5944 (p0) REVERT: C 303 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6918 (mt) REVERT: C 319 ARG cc_start: 0.7023 (ttm110) cc_final: 0.5564 (tpt170) REVERT: C 360 ASN cc_start: 0.7661 (t0) cc_final: 0.6939 (p0) REVERT: C 403 ARG cc_start: 0.6731 (ttp-170) cc_final: 0.5501 (mpt180) REVERT: C 428 ASP cc_start: 0.7635 (p0) cc_final: 0.7331 (p0) REVERT: C 513 LEU cc_start: 0.7968 (mt) cc_final: 0.7633 (mt) REVERT: C 584 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.6395 (mm) REVERT: C 612 TYR cc_start: 0.8668 (m-80) cc_final: 0.8353 (m-80) REVERT: C 731 MET cc_start: 0.9034 (ptm) cc_final: 0.8744 (ptm) REVERT: C 784 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7582 (mt0) REVERT: C 918 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: C 964 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7975 (mtmp) REVERT: C 1138 TYR cc_start: 0.7042 (t80) cc_final: 0.6472 (m-80) outliers start: 75 outliers final: 43 residues processed: 286 average time/residue: 0.4852 time to fit residues: 165.4192 Evaluate side-chains 286 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 230 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 89 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 272 optimal weight: 0.9990 chunk 262 optimal weight: 1.9990 chunk 135 optimal weight: 0.0670 chunk 13 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN B 644 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 675 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.200731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.155383 restraints weight = 26018.715| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.57 r_work: 0.3588 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22785 Z= 0.133 Angle : 0.546 14.006 31134 Z= 0.274 Chirality : 0.045 0.181 3768 Planarity : 0.004 0.045 3906 Dihedral : 4.678 47.963 4068 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.22 % Allowed : 14.99 % Favored : 81.79 % 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: 0.39 (0.15), residues: 2760 helix: 1.57 (0.21), residues: 675 sheet: 0.48 (0.19), residues: 678 loop : -0.46 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 319 TYR 0.019 0.001 TYR A1067 PHE 0.030 0.001 PHE B 92 TRP 0.018 0.002 TRP A 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00316 (22695) covalent geometry : angle 0.50985 (30903) SS BOND : bond 0.00359 ( 39) SS BOND : angle 1.81164 ( 78) hydrogen bonds : bond 0.04789 ( 973) hydrogen bonds : angle 5.38878 ( 2802) link_BETA1-4 : bond 0.00311 ( 9) link_BETA1-4 : angle 1.21837 ( 27) link_NAG-ASN : bond 0.00401 ( 42) link_NAG-ASN : angle 2.77304 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 233 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6770 (OUTLIER) cc_final: 0.6178 (p0) REVERT: A 50 SER cc_start: 0.8423 (t) cc_final: 0.8172 (t) REVERT: A 61 ASN cc_start: 0.5021 (m-40) cc_final: 0.4049 (p0) REVERT: A 303 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6956 (mt) REVERT: A 319 ARG cc_start: 0.7296 (ttm110) cc_final: 0.6033 (tpt170) REVERT: A 357 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7804 (ptm160) REVERT: A 360 ASN cc_start: 0.7439 (t0) cc_final: 0.6847 (p0) REVERT: A 513 LEU cc_start: 0.7875 (mt) cc_final: 0.7563 (mt) REVERT: A 558 LYS cc_start: 0.8177 (ttpp) cc_final: 0.7447 (mptt) REVERT: A 576 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8416 (p) REVERT: A 584 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.7121 (mm) REVERT: A 585 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7703 (mt) REVERT: A 645 THR cc_start: 0.7537 (p) cc_final: 0.7002 (t) REVERT: A 787 GLN cc_start: 0.7987 (mt0) cc_final: 0.7561 (mt0) REVERT: A 918 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: A 979 ASP cc_start: 0.8391 (m-30) cc_final: 0.8183 (m-30) REVERT: A 1138 TYR cc_start: 0.7094 (t80) cc_final: 0.6473 (m-10) REVERT: B 40 ASP cc_start: 0.6482 (OUTLIER) cc_final: 0.5907 (p0) REVERT: B 353 TRP cc_start: 0.8729 (p-90) cc_final: 0.8430 (p-90) REVERT: B 360 ASN cc_start: 0.7581 (t0) cc_final: 0.6618 (t0) REVERT: B 364 ASP cc_start: 0.8576 (t0) cc_final: 0.8370 (t0) REVERT: B 403 ARG cc_start: 0.6535 (ttp-170) cc_final: 0.5446 (mpt180) REVERT: B 513 LEU cc_start: 0.7757 (mt) cc_final: 0.7426 (mt) REVERT: B 584 ILE cc_start: 0.6976 (OUTLIER) cc_final: 0.6140 (mm) REVERT: B 786 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7388 (mmtt) REVERT: B 886 TRP cc_start: 0.7711 (p90) cc_final: 0.7355 (p90) REVERT: B 983 ARG cc_start: 0.7938 (mtp180) cc_final: 0.7604 (mtp85) REVERT: B 995 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7252 (mpp80) REVERT: B 1010 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7723 (pt0) REVERT: B 1138 TYR cc_start: 0.7256 (t80) cc_final: 0.6568 (m-10) REVERT: C 40 ASP cc_start: 0.6429 (OUTLIER) cc_final: 0.5972 (p0) REVERT: C 303 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6925 (mt) REVERT: C 319 ARG cc_start: 0.6978 (ttm110) cc_final: 0.5508 (tpt170) REVERT: C 360 ASN cc_start: 0.7662 (t0) cc_final: 0.6941 (p0) REVERT: C 400 PHE cc_start: 0.7393 (p90) cc_final: 0.7066 (p90) REVERT: C 403 ARG cc_start: 0.6751 (ttp-170) cc_final: 0.5619 (mpt180) REVERT: C 428 ASP cc_start: 0.7657 (p0) cc_final: 0.7342 (p0) REVERT: C 513 LEU cc_start: 0.7920 (mt) cc_final: 0.7554 (mt) REVERT: C 584 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.6422 (mm) REVERT: C 612 TYR cc_start: 0.8685 (m-80) cc_final: 0.8412 (m-80) REVERT: C 731 MET cc_start: 0.9043 (ptm) cc_final: 0.8698 (ptm) REVERT: C 784 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7585 (mt0) REVERT: C 918 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: C 964 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7971 (mtmp) REVERT: C 1138 TYR cc_start: 0.7060 (t80) cc_final: 0.6643 (t80) outliers start: 74 outliers final: 43 residues processed: 286 average time/residue: 0.4777 time to fit residues: 163.7709 Evaluate side-chains 285 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 226 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 234 optimal weight: 0.1980 chunk 254 optimal weight: 0.5980 chunk 213 optimal weight: 1.9990 chunk 270 optimal weight: 0.8980 chunk 184 optimal weight: 0.2980 chunk 114 optimal weight: 0.0980 chunk 257 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 675 GLN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.202245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.156696 restraints weight = 26213.123| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.60 r_work: 0.3573 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22785 Z= 0.107 Angle : 0.520 13.534 31134 Z= 0.261 Chirality : 0.044 0.193 3768 Planarity : 0.004 0.038 3906 Dihedral : 4.588 50.133 4068 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.79 % Allowed : 15.47 % Favored : 81.74 % 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: 0.52 (0.16), residues: 2760 helix: 1.77 (0.21), residues: 669 sheet: 0.52 (0.19), residues: 672 loop : -0.40 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 319 TYR 0.019 0.001 TYR C1138 PHE 0.028 0.001 PHE B 55 TRP 0.031 0.002 TRP A 353 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00243 (22695) covalent geometry : angle 0.48548 (30903) SS BOND : bond 0.00464 ( 39) SS BOND : angle 1.60032 ( 78) hydrogen bonds : bond 0.04346 ( 973) hydrogen bonds : angle 5.25678 ( 2802) link_BETA1-4 : bond 0.00362 ( 9) link_BETA1-4 : angle 1.15342 ( 27) link_NAG-ASN : bond 0.00394 ( 42) link_NAG-ASN : angle 2.64872 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 233 time to evaluate : 0.856 Fit side-chains REVERT: A 40 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.6216 (p0) REVERT: A 50 SER cc_start: 0.8442 (t) cc_final: 0.8177 (t) REVERT: A 303 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6919 (mt) REVERT: A 357 ARG cc_start: 0.8078 (ttp80) cc_final: 0.7768 (ptm160) REVERT: A 360 ASN cc_start: 0.7401 (t0) cc_final: 0.6828 (p0) REVERT: A 513 LEU cc_start: 0.7775 (mt) cc_final: 0.7405 (mt) REVERT: A 558 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7502 (mptt) REVERT: A 576 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8397 (p) REVERT: A 585 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7683 (mt) REVERT: A 645 THR cc_start: 0.7433 (p) cc_final: 0.6921 (t) REVERT: A 787 GLN cc_start: 0.7970 (mt0) cc_final: 0.7532 (mt0) REVERT: A 918 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: A 983 ARG cc_start: 0.7969 (mtp180) cc_final: 0.7664 (ttp-110) REVERT: A 1138 TYR cc_start: 0.7049 (t80) cc_final: 0.6441 (m-10) REVERT: B 40 ASP cc_start: 0.6497 (OUTLIER) cc_final: 0.5841 (p0) REVERT: B 102 ARG cc_start: 0.6330 (mtp180) cc_final: 0.6126 (mtp180) REVERT: B 196 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7799 (m110) REVERT: B 287 ASP cc_start: 0.7700 (t0) cc_final: 0.7485 (t0) REVERT: B 302 THR cc_start: 0.7440 (m) cc_final: 0.7080 (t) REVERT: B 353 TRP cc_start: 0.8692 (p-90) cc_final: 0.8403 (p-90) REVERT: B 360 ASN cc_start: 0.7566 (t0) cc_final: 0.6559 (t0) REVERT: B 364 ASP cc_start: 0.8578 (t0) cc_final: 0.8362 (t0) REVERT: B 513 LEU cc_start: 0.7761 (mt) cc_final: 0.7510 (mt) REVERT: B 584 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6240 (mm) REVERT: B 886 TRP cc_start: 0.7693 (p90) cc_final: 0.7347 (p90) REVERT: B 983 ARG cc_start: 0.7906 (mtp180) cc_final: 0.7561 (mtp85) REVERT: B 995 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7289 (mpp80) REVERT: B 1010 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7713 (pt0) REVERT: B 1138 TYR cc_start: 0.7226 (t80) cc_final: 0.6549 (m-10) REVERT: C 40 ASP cc_start: 0.6415 (OUTLIER) cc_final: 0.5989 (p0) REVERT: C 303 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6855 (mt) REVERT: C 319 ARG cc_start: 0.7001 (ttm110) cc_final: 0.5541 (tpt170) REVERT: C 360 ASN cc_start: 0.7589 (t0) cc_final: 0.6829 (p0) REVERT: C 400 PHE cc_start: 0.7395 (p90) cc_final: 0.7050 (p90) REVERT: C 403 ARG cc_start: 0.6743 (ttp-170) cc_final: 0.5619 (mpt180) REVERT: C 428 ASP cc_start: 0.7652 (p0) cc_final: 0.7338 (p0) REVERT: C 513 LEU cc_start: 0.7958 (mt) cc_final: 0.7605 (mt) REVERT: C 584 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.6386 (mm) REVERT: C 612 TYR cc_start: 0.8659 (m-80) cc_final: 0.8412 (m-80) REVERT: C 731 MET cc_start: 0.9006 (ptm) cc_final: 0.8667 (ptm) REVERT: C 784 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7566 (mt0) REVERT: C 918 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: C 964 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7931 (mtmp) REVERT: C 1138 TYR cc_start: 0.7030 (t80) cc_final: 0.6633 (t80) outliers start: 64 outliers final: 37 residues processed: 277 average time/residue: 0.4771 time to fit residues: 158.0394 Evaluate side-chains 279 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 82 optimal weight: 0.5980 chunk 92 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 67 optimal weight: 0.0030 chunk 18 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 246 optimal weight: 0.5980 chunk 202 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 126 optimal weight: 0.0060 chunk 40 optimal weight: 5.9990 overall best weight: 0.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN B 784 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C1010 GLN C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.203801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.158581 restraints weight = 26091.313| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.60 r_work: 0.3627 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22785 Z= 0.097 Angle : 0.508 12.737 31134 Z= 0.254 Chirality : 0.044 0.180 3768 Planarity : 0.004 0.041 3906 Dihedral : 4.445 50.884 4068 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.31 % Allowed : 16.21 % Favored : 81.48 % 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: 0.67 (0.16), residues: 2760 helix: 1.96 (0.21), residues: 666 sheet: 0.51 (0.19), residues: 687 loop : -0.29 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 319 TYR 0.019 0.001 TYR A1067 PHE 0.025 0.001 PHE B 55 TRP 0.028 0.002 TRP A 353 HIS 0.003 0.000 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00213 (22695) covalent geometry : angle 0.47696 (30903) SS BOND : bond 0.00380 ( 39) SS BOND : angle 1.39542 ( 78) hydrogen bonds : bond 0.03930 ( 973) hydrogen bonds : angle 5.11380 ( 2802) link_BETA1-4 : bond 0.00358 ( 9) link_BETA1-4 : angle 1.08381 ( 27) link_NAG-ASN : bond 0.00384 ( 42) link_NAG-ASN : angle 2.52788 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 235 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6654 (OUTLIER) cc_final: 0.6278 (p0) REVERT: A 50 SER cc_start: 0.8446 (t) cc_final: 0.8186 (t) REVERT: A 303 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6984 (mt) REVERT: A 319 ARG cc_start: 0.7203 (ttm110) cc_final: 0.5875 (tpt170) REVERT: A 357 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7729 (ptm160) REVERT: A 360 ASN cc_start: 0.7358 (t0) cc_final: 0.6829 (p0) REVERT: A 513 LEU cc_start: 0.7799 (mt) cc_final: 0.7430 (mt) REVERT: A 558 LYS cc_start: 0.8228 (ttpp) cc_final: 0.7516 (mptt) REVERT: A 576 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8378 (p) REVERT: A 585 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7789 (mt) REVERT: A 787 GLN cc_start: 0.7960 (mt0) cc_final: 0.7549 (mt0) REVERT: A 918 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: A 1138 TYR cc_start: 0.7104 (t80) cc_final: 0.6500 (m-10) REVERT: B 40 ASP cc_start: 0.6468 (OUTLIER) cc_final: 0.5822 (p0) REVERT: B 287 ASP cc_start: 0.7720 (t0) cc_final: 0.7507 (t0) REVERT: B 302 THR cc_start: 0.7283 (m) cc_final: 0.6969 (t) REVERT: B 319 ARG cc_start: 0.7391 (ttm110) cc_final: 0.5940 (tpt170) REVERT: B 353 TRP cc_start: 0.8693 (p-90) cc_final: 0.8422 (p-90) REVERT: B 360 ASN cc_start: 0.7581 (t0) cc_final: 0.6582 (t0) REVERT: B 513 LEU cc_start: 0.7718 (mt) cc_final: 0.7468 (mt) REVERT: B 886 TRP cc_start: 0.7681 (p90) cc_final: 0.7362 (p90) REVERT: B 983 ARG cc_start: 0.7902 (mtp180) cc_final: 0.7572 (mtp85) REVERT: B 995 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7500 (mtm180) REVERT: B 1010 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7677 (pt0) REVERT: B 1119 ASN cc_start: 0.7541 (m-40) cc_final: 0.7187 (m-40) REVERT: B 1138 TYR cc_start: 0.7253 (t80) cc_final: 0.6574 (m-10) REVERT: C 40 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.6006 (p0) REVERT: C 303 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6823 (mt) REVERT: C 319 ARG cc_start: 0.6982 (ttm110) cc_final: 0.5606 (tpt170) REVERT: C 360 ASN cc_start: 0.7596 (t0) cc_final: 0.6848 (p0) REVERT: C 400 PHE cc_start: 0.7536 (p90) cc_final: 0.7279 (p90) REVERT: C 403 ARG cc_start: 0.6736 (ttp-170) cc_final: 0.5716 (mpt180) REVERT: C 428 ASP cc_start: 0.7648 (p0) cc_final: 0.7343 (p0) REVERT: C 513 LEU cc_start: 0.7949 (mt) cc_final: 0.7573 (mt) REVERT: C 731 MET cc_start: 0.9013 (ptm) cc_final: 0.8676 (ptm) REVERT: C 784 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: C 918 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: C 964 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7887 (mtmp) REVERT: C 995 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7760 (tpp80) REVERT: C 1138 TYR cc_start: 0.7060 (t80) cc_final: 0.6625 (t80) outliers start: 53 outliers final: 29 residues processed: 272 average time/residue: 0.5067 time to fit residues: 163.5743 Evaluate side-chains 261 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 130 optimal weight: 0.1980 chunk 249 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 89 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 236 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN A1119 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 675 GLN C1010 GLN C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.202270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.157116 restraints weight = 26103.011| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.59 r_work: 0.3603 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22785 Z= 0.119 Angle : 0.525 12.421 31134 Z= 0.263 Chirality : 0.044 0.186 3768 Planarity : 0.004 0.056 3906 Dihedral : 4.427 38.708 4067 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.27 % Allowed : 16.56 % Favored : 81.18 % 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: 0.63 (0.16), residues: 2760 helix: 1.93 (0.21), residues: 666 sheet: 0.58 (0.19), residues: 672 loop : -0.37 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 319 TYR 0.019 0.001 TYR A1067 PHE 0.024 0.001 PHE B 92 TRP 0.027 0.002 TRP A 353 HIS 0.003 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00278 (22695) covalent geometry : angle 0.49418 (30903) SS BOND : bond 0.00362 ( 39) SS BOND : angle 1.61205 ( 78) hydrogen bonds : bond 0.04351 ( 973) hydrogen bonds : angle 5.16114 ( 2802) link_BETA1-4 : bond 0.00359 ( 9) link_BETA1-4 : angle 1.10623 ( 27) link_NAG-ASN : bond 0.00365 ( 42) link_NAG-ASN : angle 2.50156 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9064.01 seconds wall clock time: 154 minutes 45.40 seconds (9285.40 seconds total)