Starting phenix.real_space_refine on Fri Mar 6 22:48:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zr7_14885/03_2026/7zr7_14885.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zr7_14885/03_2026/7zr7_14885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zr7_14885/03_2026/7zr7_14885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zr7_14885/03_2026/7zr7_14885.map" model { file = "/net/cci-nas-00/data/ceres_data/7zr7_14885/03_2026/7zr7_14885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zr7_14885/03_2026/7zr7_14885.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5153 atoms to isotropic. 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 132 5.16 5 C 19566 2.51 5 N 5048 2.21 5 O 6018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 30764 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 8281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8281 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 6 Chain: "A" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8287 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 54, 'TRANS': 1006} Chain breaks: 6 Chain: "C" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8287 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 54, 'TRANS': 1006} Chain breaks: 6 Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 940 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 120} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 783 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "D" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 927 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 783 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 937 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 120} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 783 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.94, per 1000 atoms: 0.23 Number of scatterers: 30764 At special positions: 0 Unit cell: (161.02, 157.7, 209.16, 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 132 16.00 O 6018 8.00 N 5048 7.00 C 19566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 328 " " NAG A1304 " - " ASN A 600 " " NAG A1305 " - " ASN A 613 " " NAG A1306 " - " ASN A 654 " " NAG A1307 " - " ASN A 706 " " NAG A1308 " - " ASN A1071 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 340 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 328 " " NAG B1304 " - " ASN B 600 " " NAG B1305 " - " ASN B 613 " " NAG B1306 " - " ASN B 654 " " NAG B1307 " - " ASN B 706 " " NAG B1308 " - " ASN B1071 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 340 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 328 " " NAG C1304 " - " ASN C 600 " " NAG C1305 " - " ASN C 613 " " NAG C1306 " - " ASN C 654 " " NAG C1307 " - " ASN C 706 " " NAG C1308 " - " ASN C1071 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 340 " " NAG I 1 " - " ASN B 714 " " NAG J 1 " - " ASN B 798 " " NAG K 1 " - " ASN B1095 " " NAG M 1 " - " ASN B1131 " " NAG N 1 " - " ASN A 714 " " NAG O 1 " - " ASN A 798 " " NAG P 1 " - " ASN A1095 " " NAG Q 1 " - " ASN A1131 " " NAG R 1 " - " ASN C 714 " " NAG S 1 " - " ASN C 798 " " NAG T 1 " - " ASN C1095 " " NAG U 1 " - " ASN C1131 " Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.3 seconds 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7158 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 72 sheets defined 21.7% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 382 through 387 removed outlier: 3.803A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.936A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.836A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 removed outlier: 3.603A pdb=" N ILE B 906 " --> pdb=" O ARG B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.224A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.467A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.955A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 380 through 387 removed outlier: 3.652A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.802A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.632A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 910 through 938 removed outlier: 3.507A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LYS A 918 " --> pdb=" O TYR A 914 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 938 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.533A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.612A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1029 removed outlier: 4.874A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 3.673A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 380 through 387 removed outlier: 3.652A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.802A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.631A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 907 Processing helix chain 'C' and resid 909 through 938 removed outlier: 4.224A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS C 918 " --> pdb=" O TYR C 914 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU C 919 " --> pdb=" O GLU C 915 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 938 " --> pdb=" O SER C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.533A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.612A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1029 removed outlier: 4.874A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.673A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 105 through 111 Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'E' and resid 81 through 85 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 105 through 111 Processing helix chain 'G' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.626A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.982A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.005A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.359A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.005A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL B 143 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.416A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 322 through 325 removed outlier: 6.976A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AB1, first strand: chain 'B' and resid 358 through 359 removed outlier: 7.090A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AB3, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AB4, first strand: chain 'B' and resid 661 through 664 removed outlier: 6.509A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 699 through 700 Processing sheet with id=AB6, first strand: chain 'B' and resid 709 through 712 Processing sheet with id=AB7, first strand: chain 'B' and resid 715 through 725 removed outlier: 6.936A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.371A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 785 through 786 removed outlier: 5.727A pdb=" N ILE B 785 " --> pdb=" O ASN A 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.862A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AC3, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.726A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 260 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AC5, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.787A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 143 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.492A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 322 through 325 Processing sheet with id=AD1, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AD2, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.846A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AD4, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AD5, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.427A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AD7, first strand: chain 'A' and resid 715 through 725 removed outlier: 7.070A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.589A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.520A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AE2, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.726A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA C 260 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.787A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 141 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 143 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.492A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 322 through 325 Processing sheet with id=AE9, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AF1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.846A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF3, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF4, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.426A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 708 through 712 Processing sheet with id=AF6, first strand: chain 'C' and resid 715 through 725 removed outlier: 7.070A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.589A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.520A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.301A pdb=" N GLY H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.301A pdb=" N GLY H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL H 114 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.259A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AG6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AG7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY D 10 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY D 10 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL D 114 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.259A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 9 through 13 Processing sheet with id=AH3, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AH4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AH5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL F 114 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 9 through 13 removed outlier: 6.258A pdb=" N TRP G 37 " --> pdb=" O MET G 49 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 9 through 13 Processing sheet with id=AH9, first strand: chain 'G' and resid 18 through 23 1348 hydrogen bonds defined for protein. 3612 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: 7.67 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9770 1.34 - 1.46: 7907 1.46 - 1.58: 13625 1.58 - 1.70: 3 1.70 - 1.82: 168 Bond restraints: 31473 Sorted by residual: bond pdb=" CA VAL A 317 " pdb=" C VAL A 317 " ideal model delta sigma weight residual 1.523 1.618 -0.095 1.14e-02 7.69e+03 6.91e+01 bond pdb=" N THR B 304 " pdb=" CA THR B 304 " ideal model delta sigma weight residual 1.457 1.544 -0.087 1.23e-02 6.61e+03 4.97e+01 bond pdb=" CA PHE B 303 " pdb=" C PHE B 303 " ideal model delta sigma weight residual 1.521 1.616 -0.095 1.36e-02 5.41e+03 4.89e+01 bond pdb=" N GLN A 318 " pdb=" CA GLN A 318 " ideal model delta sigma weight residual 1.453 1.548 -0.095 1.64e-02 3.72e+03 3.35e+01 bond pdb=" CA GLN A 318 " pdb=" C GLN A 318 " ideal model delta sigma weight residual 1.524 1.581 -0.057 1.28e-02 6.10e+03 1.99e+01 ... (remaining 31468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 42372 2.24 - 4.48: 430 4.48 - 6.73: 15 6.73 - 8.97: 3 8.97 - 11.21: 2 Bond angle restraints: 42822 Sorted by residual: angle pdb=" N ASN C 328 " pdb=" CA ASN C 328 " pdb=" C ASN C 328 " ideal model delta sigma weight residual 112.38 123.59 -11.21 1.22e+00 6.72e-01 8.44e+01 angle pdb=" N GLN A 318 " pdb=" CA GLN A 318 " pdb=" C GLN A 318 " ideal model delta sigma weight residual 110.39 117.76 -7.37 1.30e+00 5.92e-01 3.21e+01 angle pdb=" N ASN C 328 " pdb=" CA ASN C 328 " pdb=" CB ASN C 328 " ideal model delta sigma weight residual 110.32 101.08 9.24 1.70e+00 3.46e-01 2.96e+01 angle pdb=" N SER B 588 " pdb=" CA SER B 588 " pdb=" C SER B 588 " ideal model delta sigma weight residual 110.35 117.72 -7.37 1.40e+00 5.10e-01 2.77e+01 angle pdb=" CA VAL A 317 " pdb=" C VAL A 317 " pdb=" N GLN A 318 " ideal model delta sigma weight residual 116.30 122.11 -5.81 1.13e+00 7.83e-01 2.64e+01 ... (remaining 42817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 18419 17.73 - 35.46: 674 35.46 - 53.19: 170 53.19 - 70.92: 39 70.92 - 88.65: 16 Dihedral angle restraints: 19318 sinusoidal: 8124 harmonic: 11194 Sorted by residual: dihedral pdb=" CA THR C 596 " pdb=" C THR C 596 " pdb=" N PRO C 597 " pdb=" CA PRO C 597 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA THR A 596 " pdb=" C THR A 596 " pdb=" N PRO A 597 " pdb=" CA PRO A 597 " ideal model delta harmonic sigma weight residual 180.00 161.56 18.44 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA THR B 596 " pdb=" C THR B 596 " pdb=" N PRO B 597 " pdb=" CA PRO B 597 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 19315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4504 0.085 - 0.170: 452 0.170 - 0.255: 5 0.255 - 0.340: 2 0.340 - 0.425: 2 Chirality restraints: 4965 Sorted by residual: chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C1071 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.83 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CA VAL A 317 " pdb=" N VAL A 317 " pdb=" C VAL A 317 " pdb=" CB VAL A 317 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA ASN C 328 " pdb=" N ASN C 328 " pdb=" C ASN C 328 " pdb=" CB ASN C 328 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 4962 not shown) Planarity restraints: 5507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 340 " -0.147 2.00e-02 2.50e+03 1.56e-01 3.03e+02 pdb=" CG ASN A 340 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN A 340 " 0.068 2.00e-02 2.50e+03 pdb=" ND2 ASN A 340 " 0.224 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " -0.203 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1071 " -0.130 2.00e-02 2.50e+03 1.43e-01 2.56e+02 pdb=" CG ASN C1071 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN C1071 " 0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN C1071 " 0.225 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 340 " -0.122 2.00e-02 2.50e+03 1.27e-01 2.01e+02 pdb=" CG ASN C 340 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN C 340 " 0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN C 340 " 0.184 2.00e-02 2.50e+03 pdb=" C1 NAG C1310 " -0.163 2.00e-02 2.50e+03 ... (remaining 5504 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 338 2.61 - 3.18: 27050 3.18 - 3.75: 46131 3.75 - 4.33: 67856 4.33 - 4.90: 112975 Nonbonded interactions: 254350 Sorted by model distance: nonbonded pdb=" OD1 ASN A 537 " pdb=" OG1 THR A 546 " model vdw 2.034 3.040 nonbonded pdb=" OD1 ASN C 537 " pdb=" OG1 THR C 546 " model vdw 2.035 3.040 nonbonded pdb=" OD2 ASP B 575 " pdb=" OG1 THR B 578 " model vdw 2.040 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.044 3.040 nonbonded pdb=" O ASN B 436 " pdb=" OG SER B 440 " model vdw 2.069 3.040 ... (remaining 254345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 619 or resid 638 through 1310)) selection = chain 'B' selection = (chain 'C' and (resid 13 through 619 or resid 638 through 1310)) } ncs_group { reference = (chain 'D' and (resid 1 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 86 or (resid 87 through 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 125)) selection = (chain 'F' and (resid 1 through 13 or resid 17 through 18 or (resid 19 and (name \ N or name CA or name C or name O or name CB )) or resid 20 through 125)) selection = (chain 'H' and (resid 1 through 13 or resid 17 through 72 or (resid 73 and (name \ N or name CA or name C or name O or name CB )) or resid 74 through 86 or (resid \ 87 through 88 and (name N or name CA or name C or name O or name CB )) or resid \ 89 through 125)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.280 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 31575 Z= 0.197 Angle : 0.588 18.006 43080 Z= 0.304 Chirality : 0.045 0.425 4965 Planarity : 0.003 0.034 5465 Dihedral : 10.305 88.654 12016 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 0.75 % Allowed : 4.09 % Favored : 95.16 % 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 (0.13), residues: 3822 helix: 0.33 (0.20), residues: 721 sheet: -0.20 (0.15), residues: 1042 loop : -0.75 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1016 TYR 0.013 0.001 TYR B1064 PHE 0.012 0.001 PHE B 65 TRP 0.009 0.001 TRP B 883 HIS 0.004 0.001 HIS C1061 Details of bonding type rmsd covalent geometry : bond 0.00364 (31473) covalent geometry : angle 0.53754 (42822) SS BOND : bond 0.00219 ( 48) SS BOND : angle 0.76305 ( 96) hydrogen bonds : bond 0.13911 ( 1262) hydrogen bonds : angle 7.67951 ( 3612) link_BETA1-4 : bond 0.00216 ( 12) link_BETA1-4 : angle 0.90363 ( 36) link_NAG-ASN : bond 0.00456 ( 42) link_NAG-ASN : angle 4.38140 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 339 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.8220 (m-80) cc_final: 0.7258 (m-80) REVERT: B 88 ASP cc_start: 0.8772 (m-30) cc_final: 0.8167 (p0) REVERT: B 191 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8007 (pm20) REVERT: B 275 LYS cc_start: 0.9232 (tmtt) cc_final: 0.9018 (ptmt) REVERT: B 529 ASN cc_start: 0.8813 (t0) cc_final: 0.8612 (t0) REVERT: B 555 LYS cc_start: 0.9384 (tptt) cc_final: 0.8680 (ttpp) REVERT: B 778 VAL cc_start: 0.9587 (t) cc_final: 0.9180 (m) REVERT: B 866 MET cc_start: 0.9117 (mtt) cc_final: 0.8806 (mmt) REVERT: B 910 GLN cc_start: 0.7718 (pt0) cc_final: 0.7390 (pm20) REVERT: B 1034 SER cc_start: 0.8274 (t) cc_final: 0.7301 (p) REVERT: A 760 LEU cc_start: 0.9353 (mt) cc_final: 0.8414 (mt) REVERT: C 229 LEU cc_start: 0.8389 (mt) cc_final: 0.7916 (mp) REVERT: C 998 LEU cc_start: 0.8974 (tp) cc_final: 0.8750 (pp) REVERT: H 80 TYR cc_start: 0.8833 (m-80) cc_final: 0.8546 (m-10) REVERT: L 47 LYS cc_start: 0.8474 (tttt) cc_final: 0.7840 (mptt) REVERT: D 48 VAL cc_start: 0.6382 (t) cc_final: 0.5186 (t) REVERT: F 95 TYR cc_start: 0.8316 (m-80) cc_final: 0.8099 (m-80) outliers start: 25 outliers final: 6 residues processed: 361 average time/residue: 0.2253 time to fit residues: 126.4569 Evaluate side-chains 158 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain C residue 65 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN B 603 ASN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 ASN B1008 GLN A 490 GLN A 610 GLN A 999 GLN ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN C 962 GLN ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.083321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.053392 restraints weight = 164765.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.055246 restraints weight = 72733.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.056372 restraints weight = 44092.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.057062 restraints weight = 32235.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.057421 restraints weight = 26536.290| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31575 Z= 0.160 Angle : 0.587 10.996 43080 Z= 0.301 Chirality : 0.044 0.217 4965 Planarity : 0.004 0.049 5465 Dihedral : 6.331 54.875 5303 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.59 % Favored : 97.38 % Rotamer: Outliers : 1.53 % Allowed : 7.61 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.11 (0.13), residues: 3822 helix: 1.32 (0.19), residues: 719 sheet: -0.01 (0.15), residues: 1074 loop : -0.57 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 102 TYR 0.024 0.001 TYR A1064 PHE 0.020 0.001 PHE A 55 TRP 0.008 0.001 TRP F 36 HIS 0.005 0.001 HIS A1085 Details of bonding type rmsd covalent geometry : bond 0.00353 (31473) covalent geometry : angle 0.57469 (42822) SS BOND : bond 0.00215 ( 48) SS BOND : angle 0.59068 ( 96) hydrogen bonds : bond 0.03984 ( 1262) hydrogen bonds : angle 5.81903 ( 3612) link_BETA1-4 : bond 0.00178 ( 12) link_BETA1-4 : angle 1.07478 ( 36) link_NAG-ASN : bond 0.00267 ( 42) link_NAG-ASN : angle 2.24245 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9049 (tp) REVERT: B 55 PHE cc_start: 0.8435 (m-80) cc_final: 0.7736 (m-80) REVERT: B 88 ASP cc_start: 0.8950 (m-30) cc_final: 0.7746 (p0) REVERT: B 177 MET cc_start: -0.1443 (ttm) cc_final: -0.1680 (mtt) REVERT: B 191 GLU cc_start: 0.8619 (mt-10) cc_final: 0.7916 (pm20) REVERT: B 275 LYS cc_start: 0.9099 (tttt) cc_final: 0.8760 (ptmt) REVERT: B 510 LEU cc_start: 0.9804 (mm) cc_final: 0.9576 (tp) REVERT: B 529 ASN cc_start: 0.8924 (t0) cc_final: 0.8647 (t0) REVERT: B 555 LYS cc_start: 0.9418 (tptt) cc_final: 0.8623 (ttpp) REVERT: B 737 MET cc_start: 0.9133 (ttt) cc_final: 0.8857 (ttt) REVERT: B 866 MET cc_start: 0.9071 (mtt) cc_final: 0.8777 (mmt) REVERT: B 910 GLN cc_start: 0.7687 (pt0) cc_final: 0.7461 (pm20) REVERT: B 945 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9053 (mt) REVERT: A 737 MET cc_start: 0.9053 (tpp) cc_final: 0.8179 (tpp) REVERT: A 759 GLN cc_start: 0.8449 (pp30) cc_final: 0.7918 (pp30) REVERT: A 879 ILE cc_start: 0.9273 (mt) cc_final: 0.9048 (tt) REVERT: A 897 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8933 (mtm) REVERT: C 177 MET cc_start: -0.3270 (mtt) cc_final: -0.3621 (mtt) REVERT: C 284 ASP cc_start: 0.9106 (t0) cc_final: 0.8850 (t0) REVERT: C 375 LYS cc_start: 0.9610 (mttt) cc_final: 0.9401 (mmtt) REVERT: C 777 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8625 (mt-10) outliers start: 51 outliers final: 27 residues processed: 195 average time/residue: 0.1955 time to fit residues: 62.7094 Evaluate side-chains 148 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain L residue 23 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 63 optimal weight: 3.9990 chunk 153 optimal weight: 0.0070 chunk 352 optimal weight: 7.9990 chunk 313 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 341 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 178 optimal weight: 0.3980 chunk 195 optimal weight: 3.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 GLN C 962 GLN ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.082707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.052668 restraints weight = 164866.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.054531 restraints weight = 73284.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.055655 restraints weight = 44532.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.056339 restraints weight = 32631.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.056627 restraints weight = 26915.368| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31575 Z= 0.129 Angle : 0.524 11.602 43080 Z= 0.270 Chirality : 0.042 0.194 4965 Planarity : 0.003 0.039 5465 Dihedral : 5.640 55.635 5299 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.17 % Favored : 97.80 % Rotamer: Outliers : 1.26 % Allowed : 8.90 % Favored : 89.83 % 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: 0.22 (0.13), residues: 3822 helix: 1.75 (0.20), residues: 729 sheet: 0.25 (0.15), residues: 1055 loop : -0.46 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 102 TYR 0.025 0.001 TYR A 609 PHE 0.012 0.001 PHE B 135 TRP 0.009 0.001 TRP F 115 HIS 0.003 0.001 HIS A1085 Details of bonding type rmsd covalent geometry : bond 0.00276 (31473) covalent geometry : angle 0.51415 (42822) SS BOND : bond 0.00170 ( 48) SS BOND : angle 0.55721 ( 96) hydrogen bonds : bond 0.03611 ( 1262) hydrogen bonds : angle 5.46167 ( 3612) link_BETA1-4 : bond 0.00214 ( 12) link_BETA1-4 : angle 1.05631 ( 36) link_NAG-ASN : bond 0.00233 ( 42) link_NAG-ASN : angle 1.87923 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.8546 (m-80) cc_final: 0.7690 (m-80) REVERT: B 88 ASP cc_start: 0.9002 (m-30) cc_final: 0.8149 (p0) REVERT: B 191 GLU cc_start: 0.8603 (mt-10) cc_final: 0.7875 (pm20) REVERT: B 275 LYS cc_start: 0.9137 (tttt) cc_final: 0.8824 (ptmt) REVERT: B 510 LEU cc_start: 0.9793 (mm) cc_final: 0.9553 (mp) REVERT: B 529 ASN cc_start: 0.8961 (t0) cc_final: 0.8660 (t0) REVERT: B 555 LYS cc_start: 0.9394 (tptt) cc_final: 0.8592 (ttpp) REVERT: B 737 MET cc_start: 0.9177 (ttt) cc_final: 0.8891 (ttt) REVERT: B 945 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9072 (mt) REVERT: A 737 MET cc_start: 0.9157 (tpp) cc_final: 0.8271 (tpp) REVERT: A 759 GLN cc_start: 0.8553 (pp30) cc_final: 0.7827 (pp30) REVERT: A 760 LEU cc_start: 0.9288 (mt) cc_final: 0.8830 (mt) REVERT: A 816 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8460 (pt0) REVERT: A 897 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8973 (mtm) REVERT: A 1047 MET cc_start: 0.8681 (ptp) cc_final: 0.8166 (mtm) REVERT: C 284 ASP cc_start: 0.9128 (t0) cc_final: 0.8832 (t0) REVERT: C 375 LYS cc_start: 0.9611 (mttt) cc_final: 0.9396 (mmtt) REVERT: C 571 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8195 (p0) REVERT: C 694 MET cc_start: 0.8465 (pmm) cc_final: 0.7717 (pmm) REVERT: C 770 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7166 (tm-30) REVERT: C 777 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8477 (mt-10) REVERT: D 83 MET cc_start: 0.0679 (ptp) cc_final: 0.0358 (ptp) REVERT: G 71 ASN cc_start: 0.8366 (m-40) cc_final: 0.8082 (m-40) outliers start: 42 outliers final: 25 residues processed: 157 average time/residue: 0.1998 time to fit residues: 52.7107 Evaluate side-chains 145 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain F residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 107 optimal weight: 1.9990 chunk 313 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 161 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 345 optimal weight: 4.9990 chunk 315 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 347 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 GLN B 447 ASN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 610 GLN C1132 ASN ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.079954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.049471 restraints weight = 165866.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.051242 restraints weight = 73218.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.052312 restraints weight = 44603.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.052956 restraints weight = 32852.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.053324 restraints weight = 27362.213| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 31575 Z= 0.218 Angle : 0.578 7.356 43080 Z= 0.297 Chirality : 0.043 0.183 4965 Planarity : 0.004 0.046 5465 Dihedral : 5.306 56.777 5298 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.88 % Favored : 97.10 % Rotamer: Outliers : 1.93 % Allowed : 9.03 % Favored : 89.05 % 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: 0.24 (0.13), residues: 3822 helix: 1.81 (0.20), residues: 708 sheet: 0.27 (0.15), residues: 1066 loop : -0.45 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 992 TYR 0.018 0.001 TYR A1064 PHE 0.023 0.002 PHE F 68 TRP 0.009 0.001 TRP A 883 HIS 0.009 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00465 (31473) covalent geometry : angle 0.56842 (42822) SS BOND : bond 0.00260 ( 48) SS BOND : angle 0.73212 ( 96) hydrogen bonds : bond 0.03832 ( 1262) hydrogen bonds : angle 5.39151 ( 3612) link_BETA1-4 : bond 0.00191 ( 12) link_BETA1-4 : angle 1.38266 ( 36) link_NAG-ASN : bond 0.00449 ( 42) link_NAG-ASN : angle 1.89319 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 124 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9077 (tp) REVERT: B 55 PHE cc_start: 0.8746 (m-80) cc_final: 0.7373 (m-80) REVERT: B 88 ASP cc_start: 0.9120 (m-30) cc_final: 0.7816 (p0) REVERT: B 191 GLU cc_start: 0.8732 (mt-10) cc_final: 0.7819 (pm20) REVERT: B 200 TYR cc_start: 0.9036 (OUTLIER) cc_final: 0.8395 (t80) REVERT: B 228 ASP cc_start: 0.8615 (p0) cc_final: 0.7419 (p0) REVERT: B 737 MET cc_start: 0.9176 (ttt) cc_final: 0.8947 (ttt) REVERT: B 756 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.8351 (m-10) REVERT: A 737 MET cc_start: 0.9240 (tpp) cc_final: 0.8464 (tpp) REVERT: A 759 GLN cc_start: 0.8804 (pp30) cc_final: 0.8033 (pp30) REVERT: A 760 LEU cc_start: 0.9421 (mt) cc_final: 0.8939 (mt) REVERT: A 897 MET cc_start: 0.9275 (mtm) cc_final: 0.8966 (mtm) REVERT: A 999 GLN cc_start: 0.9023 (tt0) cc_final: 0.8507 (tm-30) REVERT: A 1007 GLN cc_start: 0.7915 (pp30) cc_final: 0.7574 (pp30) REVERT: A 1026 MET cc_start: 0.9440 (mmm) cc_final: 0.9010 (tpp) REVERT: C 284 ASP cc_start: 0.9265 (t0) cc_final: 0.8873 (t70) REVERT: C 571 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8268 (p0) REVERT: C 694 MET cc_start: 0.8743 (pmm) cc_final: 0.7919 (pmm) REVERT: C 777 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8615 (mt-10) REVERT: C 866 MET cc_start: 0.9074 (mtm) cc_final: 0.8787 (mtm) REVERT: D 46 GLU cc_start: 0.7566 (tp30) cc_final: 0.7267 (tp30) outliers start: 64 outliers final: 37 residues processed: 178 average time/residue: 0.1877 time to fit residues: 55.7479 Evaluate side-chains 150 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1132 ASN Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain F residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 147 optimal weight: 3.9990 chunk 357 optimal weight: 0.5980 chunk 149 optimal weight: 5.9990 chunk 291 optimal weight: 0.5980 chunk 366 optimal weight: 0.6980 chunk 329 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 225 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 369 optimal weight: 20.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 GLN C 954 GLN C1132 ASN ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.079187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.048782 restraints weight = 168400.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.050530 restraints weight = 74583.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.051583 restraints weight = 45658.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.052243 restraints weight = 33720.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.052590 restraints weight = 27983.510| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31575 Z= 0.211 Angle : 0.555 7.464 43080 Z= 0.287 Chirality : 0.043 0.214 4965 Planarity : 0.004 0.049 5465 Dihedral : 5.131 59.811 5298 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.46 % Rotamer: Outliers : 1.99 % Allowed : 9.51 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.13), residues: 3822 helix: 2.01 (0.20), residues: 696 sheet: 0.25 (0.15), residues: 1031 loop : -0.43 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 762 TYR 0.016 0.001 TYR A 263 PHE 0.017 0.002 PHE B 556 TRP 0.017 0.001 TRP C1099 HIS 0.006 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00451 (31473) covalent geometry : angle 0.54593 (42822) SS BOND : bond 0.00228 ( 48) SS BOND : angle 0.68212 ( 96) hydrogen bonds : bond 0.03710 ( 1262) hydrogen bonds : angle 5.39404 ( 3612) link_BETA1-4 : bond 0.00140 ( 12) link_BETA1-4 : angle 1.27768 ( 36) link_NAG-ASN : bond 0.00401 ( 42) link_NAG-ASN : angle 1.75605 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 107 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9070 (tp) REVERT: B 88 ASP cc_start: 0.9171 (m-30) cc_final: 0.7802 (p0) REVERT: B 200 TYR cc_start: 0.9069 (OUTLIER) cc_final: 0.8414 (t80) REVERT: B 228 ASP cc_start: 0.8753 (p0) cc_final: 0.7684 (p0) REVERT: B 510 LEU cc_start: 0.9634 (tp) cc_final: 0.9310 (pp) REVERT: B 737 MET cc_start: 0.9097 (ttt) cc_final: 0.8840 (ttt) REVERT: B 756 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8394 (m-10) REVERT: A 737 MET cc_start: 0.9310 (tpp) cc_final: 0.8536 (tpp) REVERT: A 759 GLN cc_start: 0.8990 (pp30) cc_final: 0.8157 (pp30) REVERT: A 760 LEU cc_start: 0.9579 (mt) cc_final: 0.9143 (mt) REVERT: A 897 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.8794 (mtm) REVERT: A 966 ASN cc_start: 0.9098 (m-40) cc_final: 0.8781 (t0) REVERT: A 999 GLN cc_start: 0.9070 (tt0) cc_final: 0.8699 (tm-30) REVERT: A 1026 MET cc_start: 0.9397 (mmm) cc_final: 0.8901 (tpp) REVERT: C 571 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8336 (p0) REVERT: C 694 MET cc_start: 0.8850 (pmm) cc_final: 0.8104 (pmm) REVERT: C 899 MET cc_start: 0.9516 (mmm) cc_final: 0.9133 (mmm) REVERT: C 1132 ASN cc_start: 0.9229 (OUTLIER) cc_final: 0.8823 (m-40) REVERT: D 38 ARG cc_start: 0.7683 (ptt-90) cc_final: 0.7341 (ptt-90) REVERT: D 83 MET cc_start: 0.0907 (ptp) cc_final: 0.0558 (ptp) REVERT: G 64 PHE cc_start: 0.7200 (m-10) cc_final: 0.6838 (m-10) outliers start: 66 outliers final: 45 residues processed: 159 average time/residue: 0.1883 time to fit residues: 50.9821 Evaluate side-chains 153 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 102 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1132 ASN Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain F residue 35 HIS Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 57 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 363 optimal weight: 20.0000 chunk 294 optimal weight: 0.9980 chunk 270 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 209 optimal weight: 0.5980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 687 GLN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 ASN B 999 GLN B1116 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN A 687 GLN A 932 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 610 GLN C 853 ASN ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.076673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.046340 restraints weight = 172365.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.047949 restraints weight = 78910.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.048924 restraints weight = 49298.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.049523 restraints weight = 36980.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.049835 restraints weight = 31062.240| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 31575 Z= 0.357 Angle : 0.739 13.751 43080 Z= 0.375 Chirality : 0.046 0.233 4965 Planarity : 0.005 0.068 5465 Dihedral : 5.757 54.946 5298 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.87 % Favored : 96.10 % Rotamer: Outliers : 2.62 % Allowed : 9.39 % Favored : 88.00 % 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: -0.10 (0.13), residues: 3822 helix: 1.35 (0.19), residues: 705 sheet: 0.03 (0.15), residues: 1096 loop : -0.58 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 56 TYR 0.021 0.002 TYR A 263 PHE 0.023 0.003 PHE B 32 TRP 0.014 0.002 TRP F 36 HIS 0.008 0.002 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00764 (31473) covalent geometry : angle 0.72674 (42822) SS BOND : bond 0.00390 ( 48) SS BOND : angle 1.09218 ( 96) hydrogen bonds : bond 0.04430 ( 1262) hydrogen bonds : angle 5.83715 ( 3612) link_BETA1-4 : bond 0.00475 ( 12) link_BETA1-4 : angle 1.88895 ( 36) link_NAG-ASN : bond 0.00765 ( 42) link_NAG-ASN : angle 2.28482 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 104 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 VAL cc_start: 0.9508 (OUTLIER) cc_final: 0.9239 (m) REVERT: B 200 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8378 (t80) REVERT: B 228 ASP cc_start: 0.8868 (p0) cc_final: 0.7754 (p0) REVERT: B 574 ARG cc_start: 0.9414 (OUTLIER) cc_final: 0.8994 (ttm-80) REVERT: B 756 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8476 (m-10) REVERT: B 999 GLN cc_start: 0.9258 (tt0) cc_final: 0.8477 (tp40) REVERT: A 737 MET cc_start: 0.9402 (tpp) cc_final: 0.8600 (tpp) REVERT: A 897 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.8983 (mtm) REVERT: A 966 ASN cc_start: 0.9079 (m-40) cc_final: 0.8704 (t0) REVERT: A 999 GLN cc_start: 0.9119 (tt0) cc_final: 0.8635 (tm-30) REVERT: C 694 MET cc_start: 0.8888 (pmm) cc_final: 0.8265 (pmm) REVERT: C 866 MET cc_start: 0.9019 (mtm) cc_final: 0.8372 (ptp) REVERT: C 899 MET cc_start: 0.9456 (mmm) cc_final: 0.9209 (mmm) REVERT: C 1047 MET cc_start: 0.8675 (ptt) cc_final: 0.8259 (mtm) REVERT: C 1132 ASN cc_start: 0.9465 (OUTLIER) cc_final: 0.9157 (m-40) REVERT: L 105 LYS cc_start: 0.9339 (mmtm) cc_final: 0.9100 (tptt) REVERT: D 38 ARG cc_start: 0.7831 (ptt-90) cc_final: 0.7417 (ptt-90) REVERT: E 97 LYS cc_start: 0.9215 (pttt) cc_final: 0.8850 (tmtt) REVERT: G 96 ASN cc_start: 0.9020 (m-40) cc_final: 0.8703 (t0) outliers start: 87 outliers final: 62 residues processed: 177 average time/residue: 0.1915 time to fit residues: 56.9950 Evaluate side-chains 163 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 95 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 516 HIS Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1132 ASN Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 128 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 294 optimal weight: 0.6980 chunk 45 optimal weight: 0.0770 chunk 379 optimal weight: 7.9990 chunk 300 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 1 optimal weight: 0.0770 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 687 GLN B 759 GLN ** B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN A 610 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.078583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.048282 restraints weight = 167220.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.050034 restraints weight = 73105.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.051107 restraints weight = 44521.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.051754 restraints weight = 32773.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.052163 restraints weight = 27140.483| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31575 Z= 0.117 Angle : 0.530 13.830 43080 Z= 0.270 Chirality : 0.043 0.192 4965 Planarity : 0.003 0.045 5465 Dihedral : 4.963 51.718 5298 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.12 % Rotamer: Outliers : 1.53 % Allowed : 10.83 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.14), residues: 3822 helix: 1.85 (0.20), residues: 720 sheet: 0.16 (0.15), residues: 1078 loop : -0.42 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 992 TYR 0.015 0.001 TYR C1064 PHE 0.018 0.001 PHE F 68 TRP 0.019 0.001 TRP F 36 HIS 0.004 0.001 HIS A1085 Details of bonding type rmsd covalent geometry : bond 0.00252 (31473) covalent geometry : angle 0.52315 (42822) SS BOND : bond 0.00174 ( 48) SS BOND : angle 0.63112 ( 96) hydrogen bonds : bond 0.03507 ( 1262) hydrogen bonds : angle 5.30754 ( 3612) link_BETA1-4 : bond 0.00255 ( 12) link_BETA1-4 : angle 0.96139 ( 36) link_NAG-ASN : bond 0.00242 ( 42) link_NAG-ASN : angle 1.57878 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 111 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8525 (t80) REVERT: B 228 ASP cc_start: 0.8850 (p0) cc_final: 0.7676 (p0) REVERT: B 510 LEU cc_start: 0.9640 (tp) cc_final: 0.9266 (pp) REVERT: B 574 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8775 (ttm-80) REVERT: B 737 MET cc_start: 0.9016 (ttt) cc_final: 0.8708 (ttt) REVERT: B 999 GLN cc_start: 0.9190 (tt0) cc_final: 0.8529 (tp-100) REVERT: A 104 TRP cc_start: 0.7521 (m-90) cc_final: 0.6941 (m-90) REVERT: A 737 MET cc_start: 0.9430 (tpp) cc_final: 0.8621 (tpp) REVERT: A 759 GLN cc_start: 0.9213 (pp30) cc_final: 0.8825 (pp30) REVERT: A 897 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8705 (mtm) REVERT: A 999 GLN cc_start: 0.9069 (tt0) cc_final: 0.8531 (tm-30) REVERT: C 694 MET cc_start: 0.8855 (pmm) cc_final: 0.7945 (pmm) REVERT: C 770 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7270 (tm-30) REVERT: C 866 MET cc_start: 0.9078 (mtm) cc_final: 0.8848 (mtm) REVERT: C 1047 MET cc_start: 0.8714 (ptt) cc_final: 0.8426 (mtm) REVERT: L 97 LYS cc_start: 0.8836 (pttt) cc_final: 0.8586 (tmtt) REVERT: L 105 LYS cc_start: 0.9304 (mmtm) cc_final: 0.9037 (tptt) REVERT: D 38 ARG cc_start: 0.7922 (ptt-90) cc_final: 0.7460 (ptt-90) REVERT: E 97 LYS cc_start: 0.9159 (pttt) cc_final: 0.8810 (tmtt) REVERT: G 96 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8632 (t0) outliers start: 51 outliers final: 37 residues processed: 147 average time/residue: 0.1950 time to fit residues: 48.1348 Evaluate side-chains 145 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 516 HIS Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 96 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 151 optimal weight: 4.9990 chunk 341 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 342 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.076723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.046576 restraints weight = 169506.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.048224 restraints weight = 75314.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.049243 restraints weight = 46374.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.049838 restraints weight = 34264.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.050234 restraints weight = 28595.764| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 31575 Z= 0.272 Angle : 0.622 10.137 43080 Z= 0.316 Chirality : 0.043 0.202 4965 Planarity : 0.004 0.049 5465 Dihedral : 5.193 57.144 5297 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 1.74 % Allowed : 10.95 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.13), residues: 3822 helix: 1.62 (0.20), residues: 724 sheet: 0.07 (0.15), residues: 1099 loop : -0.46 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.018 0.002 TYR A 738 PHE 0.028 0.002 PHE B 512 TRP 0.013 0.001 TRP A 64 HIS 0.006 0.001 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.00580 (31473) covalent geometry : angle 0.61253 (42822) SS BOND : bond 0.00319 ( 48) SS BOND : angle 0.84365 ( 96) hydrogen bonds : bond 0.03900 ( 1262) hydrogen bonds : angle 5.51581 ( 3612) link_BETA1-4 : bond 0.00232 ( 12) link_BETA1-4 : angle 1.46036 ( 36) link_NAG-ASN : bond 0.00522 ( 42) link_NAG-ASN : angle 1.94950 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 106 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8734 (t80) REVERT: B 510 LEU cc_start: 0.9760 (tp) cc_final: 0.9259 (pp) REVERT: B 574 ARG cc_start: 0.9331 (OUTLIER) cc_final: 0.8996 (ttm-80) REVERT: B 737 MET cc_start: 0.9074 (ttt) cc_final: 0.8791 (ttt) REVERT: B 999 GLN cc_start: 0.9220 (tt0) cc_final: 0.8559 (tp-100) REVERT: A 737 MET cc_start: 0.9422 (tpp) cc_final: 0.8556 (tpp) REVERT: A 897 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.8841 (mtm) REVERT: A 999 GLN cc_start: 0.9175 (tt0) cc_final: 0.8798 (tm-30) REVERT: C 694 MET cc_start: 0.8866 (pmm) cc_final: 0.8097 (pmm) REVERT: C 866 MET cc_start: 0.9075 (mtm) cc_final: 0.8825 (mtm) REVERT: L 97 LYS cc_start: 0.9035 (pttt) cc_final: 0.8814 (tmtt) REVERT: D 38 ARG cc_start: 0.7887 (ptt-90) cc_final: 0.7390 (ptt-90) REVERT: E 97 LYS cc_start: 0.9261 (pttt) cc_final: 0.8880 (tmtt) REVERT: G 96 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8712 (t0) outliers start: 58 outliers final: 49 residues processed: 147 average time/residue: 0.1947 time to fit residues: 48.0500 Evaluate side-chains 155 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 102 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 516 HIS Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1047 MET Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 96 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 180 optimal weight: 0.5980 chunk 209 optimal weight: 0.8980 chunk 307 optimal weight: 0.7980 chunk 356 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 265 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 335 optimal weight: 0.7980 chunk 364 optimal weight: 10.0000 chunk 373 optimal weight: 9.9990 chunk 232 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 318 GLN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.077590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.047642 restraints weight = 167277.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.049336 restraints weight = 74161.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.050370 restraints weight = 45226.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.050968 restraints weight = 33295.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.051372 restraints weight = 27767.098| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31575 Z= 0.145 Angle : 0.533 10.714 43080 Z= 0.272 Chirality : 0.042 0.184 4965 Planarity : 0.003 0.044 5465 Dihedral : 4.821 49.242 5297 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.33 % Favored : 97.65 % Rotamer: Outliers : 1.59 % Allowed : 11.25 % Favored : 87.15 % 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: 0.27 (0.14), residues: 3822 helix: 1.91 (0.20), residues: 717 sheet: 0.16 (0.15), residues: 1077 loop : -0.39 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 902 TYR 0.015 0.001 TYR A 738 PHE 0.023 0.001 PHE B 512 TRP 0.021 0.001 TRP F 36 HIS 0.003 0.001 HIS A1085 Details of bonding type rmsd covalent geometry : bond 0.00312 (31473) covalent geometry : angle 0.52618 (42822) SS BOND : bond 0.00186 ( 48) SS BOND : angle 0.60566 ( 96) hydrogen bonds : bond 0.03516 ( 1262) hydrogen bonds : angle 5.26686 ( 3612) link_BETA1-4 : bond 0.00203 ( 12) link_BETA1-4 : angle 0.99764 ( 36) link_NAG-ASN : bond 0.00247 ( 42) link_NAG-ASN : angle 1.62935 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 105 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.8676 (t80) REVERT: B 574 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8655 (ttm-80) REVERT: B 737 MET cc_start: 0.9023 (ttt) cc_final: 0.8717 (ttt) REVERT: B 999 GLN cc_start: 0.9205 (tt0) cc_final: 0.8564 (tp-100) REVERT: A 104 TRP cc_start: 0.7559 (m-90) cc_final: 0.7007 (m-90) REVERT: A 737 MET cc_start: 0.9431 (tpp) cc_final: 0.8485 (tpp) REVERT: A 897 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.8760 (mtm) REVERT: A 999 GLN cc_start: 0.9150 (tt0) cc_final: 0.8596 (tm-30) REVERT: A 1047 MET cc_start: 0.8691 (ptp) cc_final: 0.8256 (mtm) REVERT: C 694 MET cc_start: 0.8857 (pmm) cc_final: 0.7922 (pmm) REVERT: C 770 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7430 (tm-30) REVERT: C 866 MET cc_start: 0.8997 (mtm) cc_final: 0.8742 (mtm) REVERT: C 1047 MET cc_start: 0.8907 (ptp) cc_final: 0.8681 (mtm) REVERT: L 85 GLU cc_start: 0.9472 (OUTLIER) cc_final: 0.8998 (pt0) REVERT: L 97 LYS cc_start: 0.9017 (pttt) cc_final: 0.8807 (tmtt) REVERT: L 105 LYS cc_start: 0.9411 (mmtm) cc_final: 0.9051 (tptt) REVERT: D 38 ARG cc_start: 0.8105 (ptt-90) cc_final: 0.7647 (ptt-90) REVERT: E 97 LYS cc_start: 0.9285 (pttt) cc_final: 0.8953 (tmtt) REVERT: G 96 ASN cc_start: 0.9028 (OUTLIER) cc_final: 0.8702 (t0) outliers start: 53 outliers final: 42 residues processed: 145 average time/residue: 0.1963 time to fit residues: 47.8400 Evaluate side-chains 149 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 102 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 516 HIS Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 96 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 275 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 324 optimal weight: 7.9990 chunk 366 optimal weight: 0.6980 chunk 249 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 201 optimal weight: 0.3980 chunk 140 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.077565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.047559 restraints weight = 165696.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.049262 restraints weight = 72674.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.050293 restraints weight = 44206.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.050941 restraints weight = 32450.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.051291 restraints weight = 26849.420| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31575 Z= 0.137 Angle : 0.526 10.430 43080 Z= 0.267 Chirality : 0.042 0.181 4965 Planarity : 0.003 0.043 5465 Dihedral : 4.477 34.060 5297 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.72 % Favored : 97.25 % Rotamer: Outliers : 1.53 % Allowed : 11.25 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.38 (0.14), residues: 3822 helix: 2.09 (0.20), residues: 710 sheet: 0.23 (0.15), residues: 1071 loop : -0.35 (0.14), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 574 TYR 0.015 0.001 TYR A1064 PHE 0.022 0.001 PHE B 512 TRP 0.034 0.001 TRP F 36 HIS 0.003 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00296 (31473) covalent geometry : angle 0.51815 (42822) SS BOND : bond 0.00219 ( 48) SS BOND : angle 0.56625 ( 96) hydrogen bonds : bond 0.03441 ( 1262) hydrogen bonds : angle 5.12361 ( 3612) link_BETA1-4 : bond 0.00167 ( 12) link_BETA1-4 : angle 1.04034 ( 36) link_NAG-ASN : bond 0.00229 ( 42) link_NAG-ASN : angle 1.65513 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 108 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.8580 (t80) REVERT: B 510 LEU cc_start: 0.9744 (tp) cc_final: 0.9225 (pp) REVERT: B 574 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8575 (ttm-80) REVERT: B 737 MET cc_start: 0.8989 (ttt) cc_final: 0.8681 (ttt) REVERT: B 999 GLN cc_start: 0.9217 (tt0) cc_final: 0.8573 (tp-100) REVERT: A 104 TRP cc_start: 0.7553 (m-90) cc_final: 0.7010 (m-90) REVERT: A 737 MET cc_start: 0.9437 (tpp) cc_final: 0.8513 (tpp) REVERT: A 897 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.8777 (mtm) REVERT: A 999 GLN cc_start: 0.9125 (tt0) cc_final: 0.8653 (tm-30) REVERT: A 1047 MET cc_start: 0.8607 (ptp) cc_final: 0.8118 (mtm) REVERT: C 694 MET cc_start: 0.8838 (pmm) cc_final: 0.8004 (pmm) REVERT: C 770 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7387 (tm-30) REVERT: L 97 LYS cc_start: 0.9040 (pttt) cc_final: 0.8832 (tmtt) REVERT: L 105 LYS cc_start: 0.9446 (mmtm) cc_final: 0.9067 (tptp) REVERT: D 38 ARG cc_start: 0.8187 (ptt-90) cc_final: 0.7765 (ptt-90) REVERT: E 97 LYS cc_start: 0.9381 (pttt) cc_final: 0.9141 (tmtt) REVERT: G 96 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8745 (t0) outliers start: 51 outliers final: 42 residues processed: 146 average time/residue: 0.1999 time to fit residues: 48.7846 Evaluate side-chains 151 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 105 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 96 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 239 optimal weight: 1.9990 chunk 343 optimal weight: 20.0000 chunk 61 optimal weight: 0.5980 chunk 208 optimal weight: 0.0050 chunk 329 optimal weight: 9.9990 chunk 279 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 286 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.077395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.047423 restraints weight = 166866.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.049118 restraints weight = 73282.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.050149 restraints weight = 44496.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.050779 restraints weight = 32658.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.051115 restraints weight = 27061.717| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31575 Z= 0.146 Angle : 0.526 10.198 43080 Z= 0.267 Chirality : 0.042 0.173 4965 Planarity : 0.003 0.042 5465 Dihedral : 4.392 33.645 5297 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.28 % Rotamer: Outliers : 1.50 % Allowed : 11.31 % Favored : 87.18 % 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: 0.40 (0.14), residues: 3822 helix: 2.10 (0.20), residues: 711 sheet: 0.25 (0.15), residues: 1070 loop : -0.33 (0.14), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 67 TYR 0.013 0.001 TYR A 262 PHE 0.019 0.001 PHE B 512 TRP 0.018 0.001 TRP F 36 HIS 0.003 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00316 (31473) covalent geometry : angle 0.51885 (42822) SS BOND : bond 0.00177 ( 48) SS BOND : angle 0.57272 ( 96) hydrogen bonds : bond 0.03413 ( 1262) hydrogen bonds : angle 5.08171 ( 3612) link_BETA1-4 : bond 0.00178 ( 12) link_BETA1-4 : angle 1.04245 ( 36) link_NAG-ASN : bond 0.00250 ( 42) link_NAG-ASN : angle 1.62883 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7144.11 seconds wall clock time: 123 minutes 49.78 seconds (7429.78 seconds total)