Starting phenix.real_space_refine on Sun Jul 5 19:41:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cim_16678/07_2026/8cim_16678.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cim_16678/07_2026/8cim_16678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8cim_16678/07_2026/8cim_16678.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cim_16678/07_2026/8cim_16678.cif" model { file = "/net/cci-nas-00/data/ceres_data/8cim_16678/07_2026/8cim_16678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cim_16678/07_2026/8cim_16678.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cim_16678/07_2026/8cim_16678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cim_16678/07_2026/8cim_16678.map" } resolution = 3.0 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 19026 2.51 5 N 4938 2.21 5 O 5835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.07s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29928 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7997 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 48, 'TRANS': 973} Chain breaks: 8 Chain: "B" Number of atoms: 7997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7997 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 48, 'TRANS': 973} Chain breaks: 8 Chain: "C" Number of atoms: 7997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7997 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 48, 'TRANS': 973} Chain breaks: 8 Chain: "D" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 948 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 948 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "G" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 948 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.17, per 1000 atoms: 0.21 Number of scatterers: 29928 At special positions: 0 Unit cell: (135.106, 140.218, 187.687, 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 129 16.00 O 5835 8.00 N 4938 7.00 C 19026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 163 " 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=2.02 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 B 128 " - pdb=" SG CYS B 163 " 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=2.02 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 C 128 " - pdb=" SG CYS C 163 " 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=2.02 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 D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 58 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 600 " " NAG A1304 " - " ASN A 613 " " NAG A1305 " - " ASN A 654 " " NAG A1306 " - " ASN A 706 " " NAG A1307 " - " ASN A1071 " " NAG A1308 " - " ASN A 328 " " NAG B1301 " - " ASN B 58 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 600 " " NAG B1304 " - " ASN B 613 " " NAG B1305 " - " ASN B 654 " " NAG B1306 " - " ASN B 706 " " NAG B1307 " - " ASN B1071 " " NAG B1308 " - " ASN B 328 " " NAG C1301 " - " ASN C 58 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 600 " " NAG C1304 " - " ASN C 613 " " NAG C1305 " - " ASN C 654 " " NAG C1306 " - " ASN C 706 " " NAG C1307 " - " ASN C1071 " " NAG C1308 " - " ASN C 328 " " NAG I 1 " - " ASN A 714 " " NAG J 1 " - " ASN A 798 " " NAG K 1 " - " ASN A1095 " " NAG M 1 " - " ASN A1131 " " NAG N 1 " - " ASN B 714 " " NAG O 1 " - " ASN B 798 " " NAG P 1 " - " ASN B1095 " " NAG Q 1 " - " ASN B1131 " " 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 1.4 seconds 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6990 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 60 sheets defined 22.1% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.571A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.575A pdb=" N PHE A 368 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.668A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.994A pdb=" N SER A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.647A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 removed outlier: 3.531A pdb=" N VAL A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 853 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.094A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 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 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.210A pdb=" N VAL A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.055A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.581A pdb=" N PHE B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.575A pdb=" N PHE B 368 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 386 removed outlier: 3.657A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.001A pdb=" N SER B 405 " --> pdb=" O ASN B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.652A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.523A pdb=" N VAL B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 853 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.078A 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 1030 removed outlier: 4.191A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 4.052A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.579A pdb=" N PHE C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.574A pdb=" N PHE C 368 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.666A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 3.997A pdb=" N SER C 405 " --> pdb=" O ASN C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.651A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 removed outlier: 3.514A pdb=" N VAL C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 853 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.090A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 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 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.198A pdb=" N VAL C 988 " --> pdb=" O VAL C 984 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 4.056A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.799A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.100A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.790A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.110A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.768A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.126A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 27 removed outlier: 7.616A pdb=" N ASN A 58 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR A 266 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N SER A 202 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.614A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 52 removed outlier: 3.935A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.893A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN A 118 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 316 removed outlier: 6.746A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.178A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE A 562 " --> pdb=" O PHE C 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA8, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.693A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB1, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB2, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.275A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 701 Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 712 removed outlier: 3.813A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 725 removed outlier: 6.970A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.555A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 removed outlier: 5.795A pdb=" N ILE A 785 " --> pdb=" O ASN B 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.528A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 23 through 27 removed outlier: 7.615A pdb=" N ASN B 58 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR B 266 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N SER B 202 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.648A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 44 through 52 removed outlier: 3.917A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.902A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN B 118 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 308 through 316 removed outlier: 6.757A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AC6, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.688A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC8, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AC9, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.277A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 709 through 712 removed outlier: 3.826A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 715 through 725 removed outlier: 6.993A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.550A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 785 through 787 removed outlier: 5.819A pdb=" N ILE B 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.530A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 23 through 27 removed outlier: 7.615A pdb=" N ASN C 58 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR C 266 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 226 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N SER C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 44 through 52 removed outlier: 3.900A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 82 removed outlier: 6.895A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN C 118 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 308 through 316 removed outlier: 6.755A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AE2, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.696A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE4, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AE5, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.259A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 709 through 712 removed outlier: 3.807A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 725 removed outlier: 6.979A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.575A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.528A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.390A pdb=" N GLU D 10 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.390A pdb=" N GLU D 10 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG D 98 " --> pdb=" O PRO D 115 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.730A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.821A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AF7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.381A pdb=" N GLU F 10 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.381A pdb=" N GLU F 10 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG F 98 " --> pdb=" O PRO F 115 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.743A pdb=" N ASP G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.825A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AG3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.348A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.348A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG H 98 " --> pdb=" O PRO H 115 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.705A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.663A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 1233 hydrogen bonds defined for protein. 3261 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: 8.21 Time building geometry restraints manager: 3.34 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: 9522 1.34 - 1.46: 7104 1.46 - 1.58: 13800 1.58 - 1.69: 0 1.69 - 1.81: 162 Bond restraints: 30588 Sorted by residual: bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 ... (remaining 30583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 40633 1.53 - 3.05: 816 3.05 - 4.58: 87 4.58 - 6.10: 18 6.10 - 7.63: 8 Bond angle restraints: 41562 Sorted by residual: angle pdb=" N GLY A1090 " pdb=" CA GLY A1090 " pdb=" C GLY A1090 " ideal model delta sigma weight residual 110.43 114.43 -4.00 1.35e+00 5.49e-01 8.78e+00 angle pdb=" N GLY C1090 " pdb=" CA GLY C1090 " pdb=" C GLY C1090 " ideal model delta sigma weight residual 110.43 114.38 -3.95 1.35e+00 5.49e-01 8.54e+00 angle pdb=" N GLY B1090 " pdb=" CA GLY B1090 " pdb=" C GLY B1090 " ideal model delta sigma weight residual 110.43 114.37 -3.94 1.35e+00 5.49e-01 8.50e+00 angle pdb=" C THR C 312 " pdb=" N SER C 313 " pdb=" CA SER C 313 " ideal model delta sigma weight residual 122.20 117.37 4.83 1.72e+00 3.38e-01 7.88e+00 angle pdb=" C THR B 312 " pdb=" N SER B 313 " pdb=" CA SER B 313 " ideal model delta sigma weight residual 122.39 117.85 4.54 1.64e+00 3.72e-01 7.67e+00 ... (remaining 41557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 16983 18.00 - 35.99: 681 35.99 - 53.99: 92 53.99 - 71.99: 22 71.99 - 89.98: 9 Dihedral angle restraints: 17787 sinusoidal: 6894 harmonic: 10893 Sorted by residual: 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 180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01 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 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+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 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 17784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4199 0.067 - 0.133: 598 0.133 - 0.200: 30 0.200 - 0.266: 0 0.266 - 0.333: 3 Chirality restraints: 4830 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 600 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 600 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 600 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 4827 not shown) Planarity restraints: 5331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 13 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO H 14 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 13 " -0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO F 14 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO F 14 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 14 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 13 " 0.023 5.00e-02 4.00e+02 3.55e-02 2.01e+00 pdb=" N PRO D 14 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.020 5.00e-02 4.00e+02 ... (remaining 5328 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1702 2.73 - 3.27: 28062 3.27 - 3.81: 47356 3.81 - 4.36: 59248 4.36 - 4.90: 104710 Nonbonded interactions: 241078 Sorted by model distance: nonbonded pdb=" N ASP D 114 " pdb=" OD1 ASP D 114 " model vdw 2.186 3.120 nonbonded pdb=" N ASP F 114 " pdb=" OD1 ASP F 114 " model vdw 2.190 3.120 nonbonded pdb=" N ASP H 114 " pdb=" OD1 ASP H 114 " model vdw 2.201 3.120 nonbonded pdb=" O THR A 390 " pdb=" OG1 THR A 520 " model vdw 2.236 3.040 nonbonded pdb=" O THR C 390 " pdb=" OG1 THR C 520 " model vdw 2.239 3.040 ... (remaining 241073 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.030 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 0.052 30681 Z= 0.189 Angle : 0.548 7.631 41796 Z= 0.276 Chirality : 0.046 0.333 4830 Planarity : 0.004 0.037 5295 Dihedral : 10.116 89.984 10662 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.95 % Allowed : 3.78 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.01 (0.14), residues: 3699 helix: 1.90 (0.20), residues: 684 sheet: 0.14 (0.17), residues: 963 loop : -0.70 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 400 TYR 0.018 0.001 TYR A 492 PHE 0.014 0.001 PHE B 374 TRP 0.013 0.001 TRP B 433 HIS 0.004 0.001 HIS C1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (30588) covalent geometry : angle 0.53985 / 0.27 (41562) SS BOND : bond 0.00289 / 0.17 ( 45) SS BOND : angle 0.73324 / 0.48 ( 90) hydrogen bonds : bond 0.13830 / 8.79 ( 1221) hydrogen bonds : angle 6.80738 / 4.70 ( 3261) link_BETA1-4 : bond 0.00256 / 0.14 ( 12) link_BETA1-4 : angle 0.95540 / 0.62 ( 36) link_NAG-ASN : bond 0.00263 / 0.16 ( 36) link_NAG-ASN : angle 1.83719 / 1.17 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 495 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7297 (OUTLIER) cc_final: 0.7033 (p) REVERT: A 87 VAL cc_start: 0.8858 (t) cc_final: 0.8569 (p) REVERT: A 302 SER cc_start: 0.9045 (t) cc_final: 0.8830 (p) REVERT: A 311 GLN cc_start: 0.7719 (tt0) cc_final: 0.7485 (tp-100) REVERT: A 336 ASP cc_start: 0.7947 (m-30) cc_final: 0.7541 (m-30) REVERT: A 340 ASN cc_start: 0.7722 (t0) cc_final: 0.7428 (p0) REVERT: A 354 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7985 (ttp80) REVERT: A 513 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6289 (tt0) REVERT: A 526 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7632 (mptt) REVERT: A 1014 GLU cc_start: 0.8405 (tt0) cc_final: 0.8159 (tt0) REVERT: B 26 THR cc_start: 0.6545 (OUTLIER) cc_final: 0.6186 (p) REVERT: B 81 LEU cc_start: 0.6909 (mm) cc_final: 0.6695 (mp) REVERT: B 87 VAL cc_start: 0.8716 (t) cc_final: 0.8313 (p) REVERT: B 302 SER cc_start: 0.9068 (t) cc_final: 0.8579 (p) REVERT: B 311 GLN cc_start: 0.7588 (tt0) cc_final: 0.7097 (tp-100) REVERT: B 322 SER cc_start: 0.8792 (p) cc_final: 0.8592 (p) REVERT: B 336 ASP cc_start: 0.7937 (m-30) cc_final: 0.7375 (m-30) REVERT: B 340 ASN cc_start: 0.7707 (t0) cc_final: 0.6979 (p0) REVERT: B 354 ARG cc_start: 0.8408 (ttp80) cc_final: 0.7915 (ttp80) REVERT: B 526 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7315 (mptt) REVERT: B 773 LYS cc_start: 0.8098 (tttt) cc_final: 0.7708 (tttm) REVERT: B 777 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7745 (mm-30) REVERT: B 947 ASP cc_start: 0.7510 (m-30) cc_final: 0.7265 (OUTLIER) REVERT: B 1014 GLU cc_start: 0.7920 (tt0) cc_final: 0.7578 (tt0) REVERT: B 1042 LYS cc_start: 0.8388 (mttt) cc_final: 0.8177 (mptt) REVERT: B 1111 ILE cc_start: 0.8196 (mm) cc_final: 0.7876 (tp) REVERT: B 1135 TYR cc_start: 0.7493 (t80) cc_final: 0.7203 (t80) REVERT: C 26 THR cc_start: 0.7125 (OUTLIER) cc_final: 0.6839 (p) REVERT: C 81 LEU cc_start: 0.7252 (mm) cc_final: 0.7022 (mp) REVERT: C 87 VAL cc_start: 0.8889 (t) cc_final: 0.8541 (p) REVERT: C 197 TYR cc_start: 0.6997 (m-80) cc_final: 0.6586 (m-10) REVERT: C 302 SER cc_start: 0.9051 (t) cc_final: 0.8777 (p) REVERT: C 311 GLN cc_start: 0.7631 (tt0) cc_final: 0.7381 (tp-100) REVERT: C 336 ASP cc_start: 0.7979 (m-30) cc_final: 0.7552 (m-30) REVERT: C 340 ASN cc_start: 0.7727 (t0) cc_final: 0.7300 (p0) REVERT: C 354 ARG cc_start: 0.8343 (ttp80) cc_final: 0.7970 (ttp80) REVERT: C 526 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7584 (mptt) REVERT: C 1014 GLU cc_start: 0.8359 (tt0) cc_final: 0.8074 (tt0) REVERT: C 1135 TYR cc_start: 0.7679 (t80) cc_final: 0.7396 (t80) REVERT: D 81 MET cc_start: 0.6939 (ttp) cc_final: 0.6592 (ttp) REVERT: H 64 PHE cc_start: 0.5923 (m-80) cc_final: 0.5581 (m-10) outliers start: 31 outliers final: 15 residues processed: 522 average time/residue: 0.6081 time to fit residues: 379.0215 Evaluate side-chains 293 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 276 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 947 ASP Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 ASN B 414 ASN ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN C 604 GLN C 898 GLN E 37 GLN F 100 GLN G 37 GLN G 38 GLN L 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.173812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.130364 restraints weight = 40230.023| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 3.73 r_work: 0.3321 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30681 Z= 0.146 Angle : 0.560 9.553 41796 Z= 0.287 Chirality : 0.045 0.250 4830 Planarity : 0.004 0.049 5295 Dihedral : 4.981 124.907 4055 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.18 % Allowed : 9.80 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.08 (0.14), residues: 3699 helix: 1.95 (0.20), residues: 687 sheet: 0.06 (0.16), residues: 1005 loop : -0.59 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 992 TYR 0.018 0.001 TYR A 753 PHE 0.015 0.001 PHE E 71 TRP 0.020 0.002 TRP F 36 HIS 0.006 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (30588) covalent geometry : angle 0.54507 / 0.28 (41562) SS BOND : bond 0.00401 / 0.28 ( 45) SS BOND : angle 1.72185 / 1.26 ( 90) hydrogen bonds : bond 0.04338 / 2.77 ( 1221) hydrogen bonds : angle 5.45267 / 3.74 ( 3261) link_BETA1-4 : bond 0.00365 / 0.22 ( 12) link_BETA1-4 : angle 0.84316 / 0.57 ( 36) link_NAG-ASN : bond 0.00389 / 0.24 ( 36) link_NAG-ASN : angle 2.09474 / 1.29 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 296 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7104 (OUTLIER) cc_final: 0.6882 (p) REVERT: A 50 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8031 (t70) REVERT: A 87 VAL cc_start: 0.8856 (t) cc_final: 0.8615 (p) REVERT: A 234 ARG cc_start: 0.8099 (mtt90) cc_final: 0.7896 (mtm-85) REVERT: A 336 ASP cc_start: 0.8096 (m-30) cc_final: 0.7813 (m-30) REVERT: A 340 ASN cc_start: 0.7815 (t0) cc_final: 0.7330 (p0) REVERT: A 354 ARG cc_start: 0.8632 (ttp80) cc_final: 0.8313 (ttp80) REVERT: A 513 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6506 (tt0) REVERT: A 526 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7760 (mptt) REVERT: A 1014 GLU cc_start: 0.8490 (tt0) cc_final: 0.8269 (tt0) REVERT: B 26 THR cc_start: 0.7054 (OUTLIER) cc_final: 0.6766 (p) REVERT: B 81 LEU cc_start: 0.7485 (mm) cc_final: 0.7243 (mp) REVERT: B 87 VAL cc_start: 0.8880 (t) cc_final: 0.8610 (p) REVERT: B 311 GLN cc_start: 0.8278 (tt0) cc_final: 0.8045 (tp-100) REVERT: B 336 ASP cc_start: 0.8082 (m-30) cc_final: 0.7805 (m-30) REVERT: B 340 ASN cc_start: 0.7872 (t0) cc_final: 0.7342 (p0) REVERT: B 354 ARG cc_start: 0.8664 (ttp80) cc_final: 0.8352 (ttp80) REVERT: B 513 GLU cc_start: 0.7505 (tt0) cc_final: 0.7255 (tt0) REVERT: B 526 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7702 (mptt) REVERT: B 773 LYS cc_start: 0.8880 (tttt) cc_final: 0.8634 (tttm) REVERT: B 897 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8300 (mtp) REVERT: B 1014 GLU cc_start: 0.8551 (tt0) cc_final: 0.8312 (tt0) REVERT: C 26 THR cc_start: 0.7174 (OUTLIER) cc_final: 0.6932 (p) REVERT: C 50 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8003 (t70) REVERT: C 81 LEU cc_start: 0.7552 (mm) cc_final: 0.7277 (mp) REVERT: C 87 VAL cc_start: 0.8856 (t) cc_final: 0.8604 (p) REVERT: C 197 TYR cc_start: 0.7041 (m-80) cc_final: 0.6626 (m-80) REVERT: C 234 ARG cc_start: 0.8029 (mtt90) cc_final: 0.7740 (mtm-85) REVERT: C 336 ASP cc_start: 0.8065 (m-30) cc_final: 0.7793 (m-30) REVERT: C 340 ASN cc_start: 0.7802 (t0) cc_final: 0.7375 (p0) REVERT: C 354 ARG cc_start: 0.8627 (ttp80) cc_final: 0.8272 (ttp80) REVERT: C 513 GLU cc_start: 0.7484 (tt0) cc_final: 0.7170 (tt0) REVERT: C 526 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7795 (mptt) REVERT: C 1014 GLU cc_start: 0.8634 (tt0) cc_final: 0.8380 (tt0) REVERT: C 1135 TYR cc_start: 0.8157 (t80) cc_final: 0.7903 (t80) REVERT: D 70 ILE cc_start: 0.7279 (mt) cc_final: 0.7066 (mp) REVERT: D 80 TYR cc_start: 0.7488 (m-10) cc_final: 0.7270 (m-10) REVERT: F 81 MET cc_start: 0.8286 (ttp) cc_final: 0.7882 (tmm) REVERT: G 37 GLN cc_start: 0.6445 (tt0) cc_final: 0.5987 (pp30) REVERT: H 64 PHE cc_start: 0.6517 (m-80) cc_final: 0.5534 (m-10) REVERT: L 33 LEU cc_start: 0.7727 (tp) cc_final: 0.7488 (tp) REVERT: L 47 LEU cc_start: 0.7514 (mt) cc_final: 0.7285 (mp) outliers start: 71 outliers final: 39 residues processed: 350 average time/residue: 0.5262 time to fit residues: 225.3506 Evaluate side-chains 303 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 40 optimal weight: 4.9990 chunk 121 optimal weight: 0.0170 chunk 184 optimal weight: 2.9990 chunk 334 optimal weight: 9.9990 chunk 330 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 331 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 249 optimal weight: 3.9990 chunk 309 optimal weight: 9.9990 chunk 212 optimal weight: 0.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN A 932 GLN B 471 GLN B 932 GLN B 962 GLN C 131 GLN D 100 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.168776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.127897 restraints weight = 39700.428| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.76 r_work: 0.3315 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30681 Z= 0.146 Angle : 0.530 8.911 41796 Z= 0.272 Chirality : 0.044 0.217 4830 Planarity : 0.004 0.054 5295 Dihedral : 4.466 49.259 4044 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.40 % Allowed : 11.21 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.14), residues: 3699 helix: 2.15 (0.21), residues: 666 sheet: 0.16 (0.17), residues: 933 loop : -0.65 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 98 TYR 0.017 0.001 TYR C1064 PHE 0.037 0.001 PHE D 29 TRP 0.040 0.002 TRP H 36 HIS 0.004 0.001 HIS B 951 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (30588) covalent geometry : angle 0.51918 / 0.27 (41562) SS BOND : bond 0.00613 / 0.37 ( 45) SS BOND : angle 1.24209 / 0.91 ( 90) hydrogen bonds : bond 0.04116 / 2.64 ( 1221) hydrogen bonds : angle 5.22259 / 3.57 ( 3261) link_BETA1-4 : bond 0.00258 / 0.15 ( 12) link_BETA1-4 : angle 0.90641 / 0.59 ( 36) link_NAG-ASN : bond 0.00268 / 0.17 ( 36) link_NAG-ASN : angle 1.88135 / 1.19 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 273 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7064 (OUTLIER) cc_final: 0.6837 (p) REVERT: A 50 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8092 (t70) REVERT: A 87 VAL cc_start: 0.8832 (t) cc_final: 0.8586 (p) REVERT: A 234 ARG cc_start: 0.8115 (mtt90) cc_final: 0.7899 (mtm-85) REVERT: A 336 ASP cc_start: 0.8050 (m-30) cc_final: 0.7781 (m-30) REVERT: A 340 ASN cc_start: 0.7847 (t0) cc_final: 0.7333 (p0) REVERT: A 354 ARG cc_start: 0.8618 (ttp80) cc_final: 0.8248 (ttp80) REVERT: A 513 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6385 (tt0) REVERT: A 526 LYS cc_start: 0.8288 (mmtt) cc_final: 0.7778 (mptt) REVERT: A 1014 GLU cc_start: 0.8473 (tt0) cc_final: 0.8265 (tt0) REVERT: B 26 THR cc_start: 0.7006 (OUTLIER) cc_final: 0.6671 (p) REVERT: B 27 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7965 (t0) REVERT: B 81 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7264 (mp) REVERT: B 87 VAL cc_start: 0.8842 (t) cc_final: 0.8573 (p) REVERT: B 336 ASP cc_start: 0.8100 (m-30) cc_final: 0.7816 (m-30) REVERT: B 340 ASN cc_start: 0.7894 (t0) cc_final: 0.7344 (p0) REVERT: B 354 ARG cc_start: 0.8659 (ttp80) cc_final: 0.8340 (ttp80) REVERT: B 463 ARG cc_start: 0.8371 (ttm110) cc_final: 0.8032 (ttm170) REVERT: B 490 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8329 (ttm170) REVERT: B 513 GLU cc_start: 0.7457 (tt0) cc_final: 0.7219 (tt0) REVERT: B 526 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7743 (mptt) REVERT: B 851 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8050 (tttm) REVERT: B 897 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8283 (mtp) REVERT: B 1014 GLU cc_start: 0.8520 (tt0) cc_final: 0.8237 (tt0) REVERT: B 1104 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7653 (mtm-85) REVERT: C 26 THR cc_start: 0.7153 (OUTLIER) cc_final: 0.6922 (p) REVERT: C 81 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7291 (mp) REVERT: C 87 VAL cc_start: 0.8843 (t) cc_final: 0.8587 (p) REVERT: C 197 TYR cc_start: 0.7035 (m-80) cc_final: 0.6517 (m-10) REVERT: C 234 ARG cc_start: 0.8037 (mtt90) cc_final: 0.7752 (mtm-85) REVERT: C 336 ASP cc_start: 0.8092 (m-30) cc_final: 0.7846 (m-30) REVERT: C 340 ASN cc_start: 0.7815 (t0) cc_final: 0.7386 (p0) REVERT: C 354 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8244 (ttp80) REVERT: C 526 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7789 (mptt) REVERT: C 793 TYR cc_start: 0.6841 (t80) cc_final: 0.6556 (t80) REVERT: C 1014 GLU cc_start: 0.8623 (tt0) cc_final: 0.8366 (tt0) REVERT: C 1135 TYR cc_start: 0.8162 (t80) cc_final: 0.7862 (t80) REVERT: G 37 GLN cc_start: 0.6395 (tt0) cc_final: 0.5933 (pp30) REVERT: H 64 PHE cc_start: 0.6511 (m-80) cc_final: 0.5531 (m-10) outliers start: 78 outliers final: 39 residues processed: 331 average time/residue: 0.4483 time to fit residues: 183.8958 Evaluate side-chains 306 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 1104 ARG Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 281 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 255 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 361 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN A 932 GLN A1122 ASN B 311 GLN B 932 GLN C 962 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.169663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.128221 restraints weight = 39399.142| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.58 r_work: 0.3333 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30681 Z= 0.121 Angle : 0.510 9.995 41796 Z= 0.259 Chirality : 0.044 0.196 4830 Planarity : 0.004 0.049 5295 Dihedral : 4.353 49.247 4042 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.61 % Allowed : 11.71 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.20 (0.14), residues: 3699 helix: 2.22 (0.21), residues: 666 sheet: 0.37 (0.17), residues: 909 loop : -0.66 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 24 TYR 0.016 0.001 TYR B1064 PHE 0.018 0.001 PHE D 29 TRP 0.026 0.001 TRP G 35 HIS 0.002 0.001 HIS C1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (30588) covalent geometry : angle 0.50078 / 0.26 (41562) SS BOND : bond 0.00212 / 0.13 ( 45) SS BOND : angle 0.96979 / 0.72 ( 90) hydrogen bonds : bond 0.03783 / 2.42 ( 1221) hydrogen bonds : angle 5.03461 / 3.44 ( 3261) link_BETA1-4 : bond 0.00321 / 0.20 ( 12) link_BETA1-4 : angle 0.83617 / 0.54 ( 36) link_NAG-ASN : bond 0.00261 / 0.16 ( 36) link_NAG-ASN : angle 1.76906 / 1.11 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 276 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7017 (OUTLIER) cc_final: 0.6811 (p) REVERT: A 50 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8129 (t70) REVERT: A 87 VAL cc_start: 0.8808 (t) cc_final: 0.8575 (p) REVERT: A 234 ARG cc_start: 0.8127 (mtt90) cc_final: 0.7892 (mtm-85) REVERT: A 336 ASP cc_start: 0.8006 (m-30) cc_final: 0.7753 (m-30) REVERT: A 340 ASN cc_start: 0.7839 (t0) cc_final: 0.7322 (p0) REVERT: A 354 ARG cc_start: 0.8572 (ttp80) cc_final: 0.8230 (ttp80) REVERT: A 513 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6453 (tt0) REVERT: A 526 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7793 (mptt) REVERT: A 793 TYR cc_start: 0.6891 (t80) cc_final: 0.6567 (t80) REVERT: B 26 THR cc_start: 0.6987 (OUTLIER) cc_final: 0.6629 (p) REVERT: B 81 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7250 (mp) REVERT: B 87 VAL cc_start: 0.8805 (t) cc_final: 0.8529 (p) REVERT: B 336 ASP cc_start: 0.8083 (m-30) cc_final: 0.7795 (m-30) REVERT: B 340 ASN cc_start: 0.7768 (t0) cc_final: 0.7263 (p0) REVERT: B 354 ARG cc_start: 0.8630 (ttp80) cc_final: 0.8328 (ttp80) REVERT: B 463 ARG cc_start: 0.8363 (ttm110) cc_final: 0.8029 (ttm170) REVERT: B 526 LYS cc_start: 0.8335 (mmtt) cc_final: 0.7766 (mptt) REVERT: B 851 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8043 (tttm) REVERT: B 974 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8440 (mp) REVERT: B 995 THR cc_start: 0.8738 (m) cc_final: 0.8485 (p) REVERT: B 1014 GLU cc_start: 0.8495 (tt0) cc_final: 0.8258 (tt0) REVERT: C 26 THR cc_start: 0.7109 (OUTLIER) cc_final: 0.6870 (p) REVERT: C 81 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7283 (mp) REVERT: C 87 VAL cc_start: 0.8813 (t) cc_final: 0.8560 (p) REVERT: C 197 TYR cc_start: 0.7040 (m-80) cc_final: 0.6541 (m-10) REVERT: C 234 ARG cc_start: 0.8064 (mtt90) cc_final: 0.7763 (mtm-85) REVERT: C 336 ASP cc_start: 0.8063 (m-30) cc_final: 0.7817 (m-30) REVERT: C 340 ASN cc_start: 0.7782 (t0) cc_final: 0.7283 (p0) REVERT: C 354 ARG cc_start: 0.8582 (ttp80) cc_final: 0.8230 (ttp80) REVERT: C 526 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7803 (mptt) REVERT: C 793 TYR cc_start: 0.6791 (t80) cc_final: 0.6498 (t80) REVERT: C 1014 GLU cc_start: 0.8561 (tt0) cc_final: 0.8323 (tt0) REVERT: C 1135 TYR cc_start: 0.8183 (t80) cc_final: 0.7872 (t80) REVERT: D 70 ILE cc_start: 0.7387 (mt) cc_final: 0.7133 (mp) REVERT: G 37 GLN cc_start: 0.6406 (tt0) cc_final: 0.5945 (pp30) REVERT: H 48 MET cc_start: 0.7706 (mtp) cc_final: 0.6997 (mtp) REVERT: H 64 PHE cc_start: 0.6433 (m-80) cc_final: 0.5551 (m-10) REVERT: L 33 LEU cc_start: 0.7971 (tp) cc_final: 0.7767 (mt) outliers start: 85 outliers final: 42 residues processed: 338 average time/residue: 0.5036 time to fit residues: 210.4694 Evaluate side-chains 302 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 252 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 934 SER Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 50 optimal weight: 4.9990 chunk 336 optimal weight: 0.6980 chunk 324 optimal weight: 30.0000 chunk 169 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 338 optimal weight: 8.9990 chunk 121 optimal weight: 0.2980 chunk 353 optimal weight: 10.0000 chunk 76 optimal weight: 0.4980 chunk 348 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 484 ASN A 932 GLN B 131 GLN B 801 GLN C 204 HIS C 311 GLN C 700 ASN C 962 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.168027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.126853 restraints weight = 39726.465| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.44 r_work: 0.3291 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30681 Z= 0.162 Angle : 0.533 9.170 41796 Z= 0.271 Chirality : 0.045 0.194 4830 Planarity : 0.004 0.051 5295 Dihedral : 4.435 49.806 4042 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.70 % Allowed : 12.47 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.14 (0.14), residues: 3699 helix: 2.11 (0.21), residues: 666 sheet: 0.36 (0.17), residues: 921 loop : -0.69 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.017 0.001 TYR B1064 PHE 0.014 0.001 PHE D 29 TRP 0.036 0.002 TRP D 36 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 (30588) covalent geometry : angle 0.52367 / 0.27 (41562) SS BOND : bond 0.00254 / 0.16 ( 45) SS BOND : angle 1.12949 / 0.84 ( 90) hydrogen bonds : bond 0.04063 / 2.61 ( 1221) hydrogen bonds : angle 5.05349 / 3.45 ( 3261) link_BETA1-4 : bond 0.00256 / 0.15 ( 12) link_BETA1-4 : angle 0.90912 / 0.58 ( 36) link_NAG-ASN : bond 0.00249 / 0.15 ( 36) link_NAG-ASN : angle 1.77739 / 1.13 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 262 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7008 (OUTLIER) cc_final: 0.6786 (p) REVERT: A 87 VAL cc_start: 0.8856 (t) cc_final: 0.8609 (p) REVERT: A 234 ARG cc_start: 0.8098 (mtt90) cc_final: 0.7854 (mtp-110) REVERT: A 336 ASP cc_start: 0.8049 (m-30) cc_final: 0.7779 (m-30) REVERT: A 340 ASN cc_start: 0.7902 (t0) cc_final: 0.7285 (p0) REVERT: A 354 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8229 (ttp80) REVERT: A 475 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.6438 (pptt) REVERT: A 513 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6527 (tt0) REVERT: A 526 LYS cc_start: 0.8349 (mmtt) cc_final: 0.7784 (mptt) REVERT: B 26 THR cc_start: 0.6925 (OUTLIER) cc_final: 0.6484 (p) REVERT: B 81 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7203 (mp) REVERT: B 87 VAL cc_start: 0.8864 (t) cc_final: 0.8577 (p) REVERT: B 336 ASP cc_start: 0.8104 (m-30) cc_final: 0.7827 (m-30) REVERT: B 340 ASN cc_start: 0.7804 (t0) cc_final: 0.7229 (p0) REVERT: B 354 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8319 (ttp80) REVERT: B 526 LYS cc_start: 0.8380 (mmtt) cc_final: 0.7792 (mptt) REVERT: B 793 TYR cc_start: 0.6940 (t80) cc_final: 0.6710 (t80) REVERT: B 851 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8038 (tttm) REVERT: B 974 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8405 (mp) REVERT: B 995 THR cc_start: 0.8764 (m) cc_final: 0.8488 (p) REVERT: B 1014 GLU cc_start: 0.8546 (tt0) cc_final: 0.8302 (tt0) REVERT: B 1104 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7675 (mtm-85) REVERT: C 26 THR cc_start: 0.7041 (OUTLIER) cc_final: 0.6791 (p) REVERT: C 81 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7221 (mp) REVERT: C 87 VAL cc_start: 0.8882 (t) cc_final: 0.8610 (p) REVERT: C 197 TYR cc_start: 0.7096 (m-80) cc_final: 0.6551 (m-10) REVERT: C 234 ARG cc_start: 0.8031 (mtt90) cc_final: 0.7723 (mtm-85) REVERT: C 336 ASP cc_start: 0.8097 (m-30) cc_final: 0.7813 (m-30) REVERT: C 340 ASN cc_start: 0.7788 (t0) cc_final: 0.7239 (p0) REVERT: C 354 ARG cc_start: 0.8604 (ttp80) cc_final: 0.8227 (ttp80) REVERT: C 526 LYS cc_start: 0.8382 (mmtt) cc_final: 0.7798 (mptt) REVERT: C 961 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8633 (mttt) REVERT: C 1014 GLU cc_start: 0.8614 (tt0) cc_final: 0.8354 (tt0) REVERT: C 1135 TYR cc_start: 0.8154 (t80) cc_final: 0.7857 (t80) REVERT: G 24 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7169 (ttm-80) REVERT: G 37 GLN cc_start: 0.6416 (tt0) cc_final: 0.5964 (pp30) REVERT: H 23 LYS cc_start: 0.7977 (tttm) cc_final: 0.7523 (ttmt) REVERT: H 48 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7081 (mtp) REVERT: H 64 PHE cc_start: 0.6460 (m-80) cc_final: 0.5587 (m-10) outliers start: 88 outliers final: 52 residues processed: 324 average time/residue: 0.4658 time to fit residues: 186.2746 Evaluate side-chains 317 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 253 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 934 SER Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 801 GLN Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1104 ARG Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 961 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 26 optimal weight: 0.7980 chunk 217 optimal weight: 4.9990 chunk 264 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 192 optimal weight: 0.2980 chunk 173 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 322 optimal weight: 10.0000 chunk 294 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 ASN A 932 GLN B 402 ASN C 204 HIS C 402 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.169441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.129065 restraints weight = 39456.461| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.03 r_work: 0.3317 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30681 Z= 0.110 Angle : 0.501 9.227 41796 Z= 0.255 Chirality : 0.043 0.180 4830 Planarity : 0.004 0.063 5295 Dihedral : 4.324 49.408 4042 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.52 % Allowed : 13.21 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 3699 helix: 2.48 (0.21), residues: 645 sheet: 0.42 (0.17), residues: 906 loop : -0.65 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 490 TYR 0.016 0.001 TYR B1064 PHE 0.012 0.001 PHE D 29 TRP 0.044 0.002 TRP H 36 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (30588) covalent geometry : angle 0.49260 / 0.25 (41562) SS BOND : bond 0.00214 / 0.14 ( 45) SS BOND : angle 0.91172 / 0.66 ( 90) hydrogen bonds : bond 0.03669 / 2.35 ( 1221) hydrogen bonds : angle 4.94607 / 3.38 ( 3261) link_BETA1-4 : bond 0.00318 / 0.20 ( 12) link_BETA1-4 : angle 0.83142 / 0.54 ( 36) link_NAG-ASN : bond 0.00242 / 0.14 ( 36) link_NAG-ASN : angle 1.70283 / 1.07 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 273 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8024 (t70) REVERT: A 87 VAL cc_start: 0.8767 (t) cc_final: 0.8523 (p) REVERT: A 197 TYR cc_start: 0.6988 (m-80) cc_final: 0.6511 (m-10) REVERT: A 336 ASP cc_start: 0.7726 (m-30) cc_final: 0.7523 (m-30) REVERT: A 340 ASN cc_start: 0.7598 (t0) cc_final: 0.7212 (p0) REVERT: A 354 ARG cc_start: 0.8410 (ttp80) cc_final: 0.8094 (ttp80) REVERT: A 475 LYS cc_start: 0.7662 (pmmt) cc_final: 0.6522 (pptt) REVERT: A 513 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6253 (tt0) REVERT: A 526 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7727 (mptt) REVERT: A 793 TYR cc_start: 0.6711 (t80) cc_final: 0.6480 (t80) REVERT: B 26 THR cc_start: 0.6818 (OUTLIER) cc_final: 0.6448 (p) REVERT: B 81 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7201 (mp) REVERT: B 87 VAL cc_start: 0.8756 (t) cc_final: 0.8471 (p) REVERT: B 234 ARG cc_start: 0.7853 (mtt90) cc_final: 0.7644 (mtm-85) REVERT: B 336 ASP cc_start: 0.7756 (m-30) cc_final: 0.7539 (m-30) REVERT: B 340 ASN cc_start: 0.7504 (t0) cc_final: 0.7196 (p0) REVERT: B 354 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8183 (ttp80) REVERT: B 475 LYS cc_start: 0.7443 (pptt) cc_final: 0.7164 (pmmt) REVERT: B 513 GLU cc_start: 0.7530 (tt0) cc_final: 0.6396 (tt0) REVERT: B 526 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7719 (mptt) REVERT: B 851 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7846 (tttm) REVERT: B 897 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7986 (mtp) REVERT: B 974 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8376 (mp) REVERT: B 995 THR cc_start: 0.8621 (m) cc_final: 0.8415 (p) REVERT: B 1014 GLU cc_start: 0.8241 (tt0) cc_final: 0.8022 (tt0) REVERT: C 26 THR cc_start: 0.7006 (OUTLIER) cc_final: 0.6794 (p) REVERT: C 81 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7173 (mp) REVERT: C 87 VAL cc_start: 0.8789 (t) cc_final: 0.8519 (p) REVERT: C 197 TYR cc_start: 0.6942 (m-80) cc_final: 0.6437 (m-10) REVERT: C 336 ASP cc_start: 0.7763 (m-30) cc_final: 0.7539 (m-30) REVERT: C 340 ASN cc_start: 0.7475 (t0) cc_final: 0.7174 (p0) REVERT: C 354 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8095 (ttp80) REVERT: C 526 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7738 (mptt) REVERT: C 1014 GLU cc_start: 0.8311 (tt0) cc_final: 0.8092 (tt0) REVERT: C 1135 TYR cc_start: 0.8107 (t80) cc_final: 0.7874 (t80) REVERT: D 80 TYR cc_start: 0.6565 (m-80) cc_final: 0.6306 (m-80) REVERT: G 24 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7221 (ttm-80) REVERT: G 37 GLN cc_start: 0.6510 (tt0) cc_final: 0.6004 (pp30) REVERT: H 23 LYS cc_start: 0.7982 (tttm) cc_final: 0.7509 (ttmt) REVERT: H 48 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7041 (mtp) REVERT: H 64 PHE cc_start: 0.6370 (m-80) cc_final: 0.5616 (m-10) REVERT: L 33 LEU cc_start: 0.8124 (tp) cc_final: 0.7880 (mt) outliers start: 82 outliers final: 48 residues processed: 332 average time/residue: 0.4491 time to fit residues: 185.9105 Evaluate side-chains 314 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 256 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 934 SER Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 75 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 362 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 932 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 HIS B 700 ASN C 204 HIS ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 HIS C 700 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.166690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.125892 restraints weight = 39509.123| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.13 r_work: 0.3269 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 30681 Z= 0.192 Angle : 0.556 10.577 41796 Z= 0.282 Chirality : 0.046 0.189 4830 Planarity : 0.004 0.060 5295 Dihedral : 4.506 51.136 4041 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.55 % Allowed : 13.43 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.06 (0.14), residues: 3699 helix: 2.03 (0.20), residues: 666 sheet: 0.32 (0.16), residues: 954 loop : -0.77 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 234 TYR 0.017 0.001 TYR B1064 PHE 0.025 0.001 PHE A 165 TRP 0.029 0.002 TRP D 36 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 (30588) covalent geometry : angle 0.54725 / 0.28 (41562) SS BOND : bond 0.00280 / 0.17 ( 45) SS BOND : angle 1.10425 / 0.80 ( 90) hydrogen bonds : bond 0.04268 / 2.74 ( 1221) hydrogen bonds : angle 5.07259 / 3.47 ( 3261) link_BETA1-4 : bond 0.00272 / 0.16 ( 12) link_BETA1-4 : angle 0.95473 / 0.61 ( 36) link_NAG-ASN : bond 0.00259 / 0.16 ( 36) link_NAG-ASN : angle 1.75003 / 1.13 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 255 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8238 (t70) REVERT: A 87 VAL cc_start: 0.8868 (t) cc_final: 0.8635 (p) REVERT: A 197 TYR cc_start: 0.7200 (m-80) cc_final: 0.6614 (m-80) REVERT: A 336 ASP cc_start: 0.8091 (m-30) cc_final: 0.7828 (m-30) REVERT: A 340 ASN cc_start: 0.7919 (t0) cc_final: 0.7268 (p0) REVERT: A 354 ARG cc_start: 0.8606 (ttp80) cc_final: 0.8250 (ttp80) REVERT: A 475 LYS cc_start: 0.7709 (pmmt) cc_final: 0.6547 (pptt) REVERT: A 513 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6520 (tt0) REVERT: A 526 LYS cc_start: 0.8410 (mmtt) cc_final: 0.7823 (mptt) REVERT: B 26 THR cc_start: 0.6811 (OUTLIER) cc_final: 0.6377 (p) REVERT: B 81 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7205 (mp) REVERT: B 87 VAL cc_start: 0.8879 (t) cc_final: 0.8592 (p) REVERT: B 234 ARG cc_start: 0.8085 (mtt90) cc_final: 0.7810 (mtm-85) REVERT: B 336 ASP cc_start: 0.8107 (m-30) cc_final: 0.7841 (m-30) REVERT: B 340 ASN cc_start: 0.7833 (t0) cc_final: 0.7236 (p0) REVERT: B 354 ARG cc_start: 0.8657 (ttp80) cc_final: 0.8308 (ttp80) REVERT: B 475 LYS cc_start: 0.7503 (pptt) cc_final: 0.7145 (pmmt) REVERT: B 513 GLU cc_start: 0.7721 (tt0) cc_final: 0.6643 (tt0) REVERT: B 526 LYS cc_start: 0.8422 (mmtt) cc_final: 0.7814 (mptt) REVERT: B 851 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8032 (tttm) REVERT: B 974 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8404 (mp) REVERT: B 1014 GLU cc_start: 0.8595 (tt0) cc_final: 0.8304 (tt0) REVERT: C 26 THR cc_start: 0.7103 (OUTLIER) cc_final: 0.6869 (p) REVERT: C 50 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8187 (t70) REVERT: C 81 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7218 (mp) REVERT: C 87 VAL cc_start: 0.8885 (t) cc_final: 0.8598 (p) REVERT: C 197 TYR cc_start: 0.7154 (m-80) cc_final: 0.6555 (m-10) REVERT: C 234 ARG cc_start: 0.8078 (mtt90) cc_final: 0.7739 (mtm-85) REVERT: C 316 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7516 (mtt-85) REVERT: C 336 ASP cc_start: 0.8084 (m-30) cc_final: 0.7822 (m-30) REVERT: C 340 ASN cc_start: 0.7825 (t0) cc_final: 0.7262 (p0) REVERT: C 354 ARG cc_start: 0.8613 (ttp80) cc_final: 0.8240 (ttp80) REVERT: C 526 LYS cc_start: 0.8461 (mmtt) cc_final: 0.7850 (mptt) REVERT: C 1014 GLU cc_start: 0.8665 (tt0) cc_final: 0.8381 (tt0) REVERT: C 1135 TYR cc_start: 0.8161 (t80) cc_final: 0.7849 (t80) REVERT: G 24 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7233 (ttm-80) REVERT: G 37 GLN cc_start: 0.6574 (tt0) cc_final: 0.6023 (pp30) REVERT: H 23 LYS cc_start: 0.8006 (tttm) cc_final: 0.7578 (tppt) REVERT: H 29 PHE cc_start: 0.7121 (t80) cc_final: 0.6701 (t80) REVERT: H 48 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7099 (mtp) REVERT: H 64 PHE cc_start: 0.6349 (m-80) cc_final: 0.5598 (m-10) outliers start: 83 outliers final: 51 residues processed: 318 average time/residue: 0.4815 time to fit residues: 189.1728 Evaluate side-chains 309 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 247 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 934 SER Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 10.0000 chunk 29 optimal weight: 0.0060 chunk 347 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 366 optimal weight: 10.0000 chunk 230 optimal weight: 0.9980 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 932 GLN B 471 GLN C 84 ASN C 204 HIS C 484 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.167852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.126497 restraints weight = 39509.072| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.40 r_work: 0.3281 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30681 Z= 0.151 Angle : 0.536 9.815 41796 Z= 0.272 Chirality : 0.044 0.172 4830 Planarity : 0.004 0.056 5295 Dihedral : 4.467 52.190 4041 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.24 % Allowed : 14.16 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.14), residues: 3699 helix: 2.09 (0.21), residues: 666 sheet: 0.35 (0.16), residues: 978 loop : -0.78 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 234 TYR 0.017 0.001 TYR B1064 PHE 0.024 0.001 PHE A 130 TRP 0.031 0.002 TRP D 36 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (30588) covalent geometry : angle 0.52673 / 0.27 (41562) SS BOND : bond 0.00258 / 0.17 ( 45) SS BOND : angle 1.15660 / 0.82 ( 90) hydrogen bonds : bond 0.03993 / 2.56 ( 1221) hydrogen bonds : angle 5.02361 / 3.44 ( 3261) link_BETA1-4 : bond 0.00281 / 0.17 ( 12) link_BETA1-4 : angle 0.87133 / 0.56 ( 36) link_NAG-ASN : bond 0.00226 / 0.13 ( 36) link_NAG-ASN : angle 1.70581 / 1.09 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 258 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8204 (t70) REVERT: A 87 VAL cc_start: 0.8867 (t) cc_final: 0.8626 (p) REVERT: A 197 TYR cc_start: 0.7178 (m-80) cc_final: 0.6580 (m-80) REVERT: A 336 ASP cc_start: 0.8040 (m-30) cc_final: 0.7789 (m-30) REVERT: A 340 ASN cc_start: 0.7894 (t0) cc_final: 0.7233 (p0) REVERT: A 354 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8243 (ttp80) REVERT: A 513 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6479 (tt0) REVERT: A 526 LYS cc_start: 0.8391 (mmtt) cc_final: 0.7800 (mptt) REVERT: A 793 TYR cc_start: 0.6927 (t80) cc_final: 0.6643 (t80) REVERT: B 26 THR cc_start: 0.6810 (OUTLIER) cc_final: 0.6372 (p) REVERT: B 81 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7158 (mp) REVERT: B 87 VAL cc_start: 0.8865 (t) cc_final: 0.8578 (p) REVERT: B 234 ARG cc_start: 0.8045 (mtt90) cc_final: 0.7772 (mtp-110) REVERT: B 336 ASP cc_start: 0.8069 (m-30) cc_final: 0.7811 (m-30) REVERT: B 340 ASN cc_start: 0.7786 (t0) cc_final: 0.7175 (p0) REVERT: B 354 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8276 (ttp80) REVERT: B 475 LYS cc_start: 0.7474 (pptt) cc_final: 0.7230 (pmmt) REVERT: B 513 GLU cc_start: 0.7747 (tt0) cc_final: 0.6708 (tt0) REVERT: B 526 LYS cc_start: 0.8415 (mmtt) cc_final: 0.7796 (mptt) REVERT: B 793 TYR cc_start: 0.6857 (t80) cc_final: 0.6632 (t80) REVERT: B 851 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8026 (tttm) REVERT: B 974 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8381 (mp) REVERT: B 1014 GLU cc_start: 0.8585 (tt0) cc_final: 0.8340 (tt0) REVERT: C 26 THR cc_start: 0.7075 (OUTLIER) cc_final: 0.6842 (p) REVERT: C 50 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8138 (t70) REVERT: C 81 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7169 (mp) REVERT: C 87 VAL cc_start: 0.8878 (t) cc_final: 0.8578 (p) REVERT: C 197 TYR cc_start: 0.7095 (m-80) cc_final: 0.6522 (m-10) REVERT: C 234 ARG cc_start: 0.8038 (mtt90) cc_final: 0.7681 (mtm-85) REVERT: C 316 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7529 (mtt-85) REVERT: C 336 ASP cc_start: 0.8059 (m-30) cc_final: 0.7791 (m-30) REVERT: C 340 ASN cc_start: 0.7763 (t0) cc_final: 0.7198 (p0) REVERT: C 354 ARG cc_start: 0.8594 (ttp80) cc_final: 0.8225 (ttp80) REVERT: C 526 LYS cc_start: 0.8454 (mmtt) cc_final: 0.7836 (mptt) REVERT: C 1014 GLU cc_start: 0.8643 (tt0) cc_final: 0.8358 (tt0) REVERT: C 1135 TYR cc_start: 0.8188 (t80) cc_final: 0.7849 (t80) REVERT: G 24 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7577 (ttt-90) REVERT: G 37 GLN cc_start: 0.6485 (tt0) cc_final: 0.5997 (pp30) REVERT: H 23 LYS cc_start: 0.7983 (tttm) cc_final: 0.7496 (ttmt) REVERT: H 29 PHE cc_start: 0.7018 (t80) cc_final: 0.6763 (t80) REVERT: H 48 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7136 (mtp) REVERT: H 64 PHE cc_start: 0.6351 (m-80) cc_final: 0.5649 (m-10) outliers start: 73 outliers final: 46 residues processed: 311 average time/residue: 0.4666 time to fit residues: 179.2672 Evaluate side-chains 303 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 246 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 934 SER Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 9.9990 chunk 28 optimal weight: 0.0040 chunk 158 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 318 optimal weight: 0.9980 chunk 105 optimal weight: 0.0010 chunk 199 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 chunk 177 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 932 GLN B 471 GLN C 204 HIS C 471 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 = 0.4123 r_free = 0.4123 target = 0.170302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.129586 restraints weight = 39407.445| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.37 r_work: 0.3332 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30681 Z= 0.092 Angle : 0.501 10.766 41796 Z= 0.252 Chirality : 0.043 0.229 4830 Planarity : 0.004 0.053 5295 Dihedral : 4.253 51.285 4041 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.66 % Allowed : 14.78 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3699 helix: 2.32 (0.21), residues: 666 sheet: 0.46 (0.17), residues: 930 loop : -0.69 (0.14), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 234 TYR 0.019 0.001 TYR L 32 PHE 0.026 0.001 PHE A 165 TRP 0.043 0.002 TRP G 35 HIS 0.004 0.000 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (30588) covalent geometry : angle 0.49270 / 0.25 (41562) SS BOND : bond 0.00196 / 0.13 ( 45) SS BOND : angle 0.94401 / 0.65 ( 90) hydrogen bonds : bond 0.03435 / 2.21 ( 1221) hydrogen bonds : angle 4.87395 / 3.33 ( 3261) link_BETA1-4 : bond 0.00348 / 0.22 ( 12) link_BETA1-4 : angle 0.81957 / 0.53 ( 36) link_NAG-ASN : bond 0.00247 / 0.14 ( 36) link_NAG-ASN : angle 1.63667 / 1.03 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 265 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8101 (t70) REVERT: A 87 VAL cc_start: 0.8827 (t) cc_final: 0.8572 (p) REVERT: A 336 ASP cc_start: 0.8017 (m-30) cc_final: 0.7801 (m-30) REVERT: A 340 ASN cc_start: 0.7786 (t0) cc_final: 0.7178 (p0) REVERT: A 354 ARG cc_start: 0.8593 (ttp80) cc_final: 0.8237 (ttp80) REVERT: A 475 LYS cc_start: 0.7753 (pmmt) cc_final: 0.6569 (pptt) REVERT: A 513 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6492 (tt0) REVERT: A 526 LYS cc_start: 0.8367 (mmtt) cc_final: 0.7748 (mptt) REVERT: A 793 TYR cc_start: 0.6850 (t80) cc_final: 0.6537 (t80) REVERT: B 26 THR cc_start: 0.6702 (OUTLIER) cc_final: 0.6264 (p) REVERT: B 81 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7207 (mp) REVERT: B 87 VAL cc_start: 0.8817 (t) cc_final: 0.8520 (p) REVERT: B 234 ARG cc_start: 0.8030 (mtt90) cc_final: 0.7717 (mtm-85) REVERT: B 336 ASP cc_start: 0.8015 (m-30) cc_final: 0.7763 (m-30) REVERT: B 340 ASN cc_start: 0.7706 (t0) cc_final: 0.7115 (p0) REVERT: B 354 ARG cc_start: 0.8617 (ttp80) cc_final: 0.8271 (ttp80) REVERT: B 513 GLU cc_start: 0.7658 (tt0) cc_final: 0.7398 (tt0) REVERT: B 526 LYS cc_start: 0.8390 (mmtt) cc_final: 0.7765 (mptt) REVERT: B 793 TYR cc_start: 0.6793 (t80) cc_final: 0.6566 (t80) REVERT: B 995 THR cc_start: 0.8752 (m) cc_final: 0.8452 (p) REVERT: B 1014 GLU cc_start: 0.8481 (tt0) cc_final: 0.8194 (tt0) REVERT: C 50 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8064 (t70) REVERT: C 81 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7177 (mp) REVERT: C 87 VAL cc_start: 0.8796 (t) cc_final: 0.8512 (p) REVERT: C 197 TYR cc_start: 0.7036 (m-80) cc_final: 0.6469 (m-10) REVERT: C 234 ARG cc_start: 0.8043 (mtt90) cc_final: 0.7712 (mtm-85) REVERT: C 336 ASP cc_start: 0.7964 (m-30) cc_final: 0.7728 (m-30) REVERT: C 340 ASN cc_start: 0.7686 (t0) cc_final: 0.7146 (p0) REVERT: C 354 ARG cc_start: 0.8562 (ttp80) cc_final: 0.8197 (ttp80) REVERT: C 526 LYS cc_start: 0.8469 (mmtt) cc_final: 0.7818 (mptt) REVERT: C 793 TYR cc_start: 0.6759 (t80) cc_final: 0.6498 (t80) REVERT: C 1014 GLU cc_start: 0.8560 (tt0) cc_final: 0.8296 (tt0) REVERT: C 1135 TYR cc_start: 0.8129 (t80) cc_final: 0.7841 (t80) REVERT: E 32 TYR cc_start: 0.6582 (m-10) cc_final: 0.6374 (m-10) REVERT: G 24 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7562 (ttt-90) REVERT: G 33 LEU cc_start: 0.7572 (mt) cc_final: 0.7220 (tt) REVERT: G 37 GLN cc_start: 0.6530 (tt0) cc_final: 0.6019 (pp30) REVERT: H 23 LYS cc_start: 0.7961 (tttm) cc_final: 0.7482 (ttmt) REVERT: H 48 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7040 (mtp) REVERT: H 64 PHE cc_start: 0.6250 (m-80) cc_final: 0.5689 (m-80) REVERT: L 32 TYR cc_start: 0.6346 (m-10) cc_final: 0.6108 (m-10) outliers start: 54 outliers final: 33 residues processed: 298 average time/residue: 0.4684 time to fit residues: 172.7615 Evaluate side-chains 294 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 308 optimal weight: 1.9990 chunk 349 optimal weight: 10.0000 chunk 310 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 329 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 289 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 359 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN C 204 HIS ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.168034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.125806 restraints weight = 39443.744| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 3.69 r_work: 0.3282 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 30681 Z= 0.198 Angle : 0.569 9.527 41796 Z= 0.288 Chirality : 0.046 0.187 4830 Planarity : 0.004 0.055 5295 Dihedral : 4.461 52.891 4040 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.66 % Allowed : 15.08 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.08 (0.14), residues: 3699 helix: 2.10 (0.21), residues: 666 sheet: 0.34 (0.16), residues: 978 loop : -0.79 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 234 TYR 0.018 0.002 TYR L 32 PHE 0.031 0.002 PHE A 130 TRP 0.043 0.002 TRP F 36 HIS 0.006 0.001 HIS G 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.20 (30588) covalent geometry : angle 0.56019 / 0.29 (41562) SS BOND : bond 0.00304 / 0.18 ( 45) SS BOND : angle 1.26063 / 0.91 ( 90) hydrogen bonds : bond 0.04254 / 2.73 ( 1221) hydrogen bonds : angle 5.04765 / 3.45 ( 3261) link_BETA1-4 : bond 0.00262 / 0.15 ( 12) link_BETA1-4 : angle 0.99999 / 0.63 ( 36) link_NAG-ASN : bond 0.00260 / 0.16 ( 36) link_NAG-ASN : angle 1.69273 / 1.10 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8144 (t70) REVERT: A 87 VAL cc_start: 0.8797 (t) cc_final: 0.8535 (p) REVERT: A 197 TYR cc_start: 0.7011 (m-80) cc_final: 0.6408 (m-80) REVERT: A 340 ASN cc_start: 0.7676 (t0) cc_final: 0.7203 (p0) REVERT: A 354 ARG cc_start: 0.8394 (ttp80) cc_final: 0.8117 (ttp80) REVERT: A 513 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6396 (tt0) REVERT: A 526 LYS cc_start: 0.8293 (mmtt) cc_final: 0.7754 (mptt) REVERT: B 26 THR cc_start: 0.6758 (OUTLIER) cc_final: 0.6349 (p) REVERT: B 81 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7165 (mp) REVERT: B 87 VAL cc_start: 0.8785 (t) cc_final: 0.8499 (p) REVERT: B 340 ASN cc_start: 0.7595 (t0) cc_final: 0.7172 (p0) REVERT: B 354 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8202 (ttp80) REVERT: B 471 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7644 (mm-40) REVERT: B 513 GLU cc_start: 0.7650 (tt0) cc_final: 0.6592 (tt0) REVERT: B 526 LYS cc_start: 0.8316 (mmtt) cc_final: 0.7774 (mptt) REVERT: B 1014 GLU cc_start: 0.8357 (tt0) cc_final: 0.8107 (tt0) REVERT: C 50 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8082 (t70) REVERT: C 81 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7146 (mp) REVERT: C 87 VAL cc_start: 0.8830 (t) cc_final: 0.8533 (p) REVERT: C 197 TYR cc_start: 0.6976 (m-80) cc_final: 0.6384 (m-10) REVERT: C 228 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7367 (pp) REVERT: C 234 ARG cc_start: 0.7874 (mtt90) cc_final: 0.7653 (mtm-85) REVERT: C 340 ASN cc_start: 0.7551 (t0) cc_final: 0.7174 (p0) REVERT: C 354 ARG cc_start: 0.8407 (ttp80) cc_final: 0.8099 (ttp80) REVERT: C 526 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7779 (mptt) REVERT: C 1014 GLU cc_start: 0.8419 (tt0) cc_final: 0.8191 (tt0) REVERT: C 1088 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7899 (mtt180) REVERT: C 1135 TYR cc_start: 0.8163 (t80) cc_final: 0.7875 (t80) REVERT: G 24 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7627 (ttt-90) REVERT: G 37 GLN cc_start: 0.6619 (tt0) cc_final: 0.6029 (pp30) REVERT: H 23 LYS cc_start: 0.7944 (tttm) cc_final: 0.7417 (ttmt) REVERT: H 29 PHE cc_start: 0.6896 (t80) cc_final: 0.6676 (t80) REVERT: H 48 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7103 (mtp) REVERT: H 64 PHE cc_start: 0.6188 (m-80) cc_final: 0.5727 (m-80) REVERT: L 32 TYR cc_start: 0.6450 (m-10) cc_final: 0.6183 (m-10) outliers start: 54 outliers final: 38 residues processed: 283 average time/residue: 0.4962 time to fit residues: 173.7860 Evaluate side-chains 288 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 240 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 934 SER Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1088 ARG Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 371 optimal weight: 0.9990 chunk 319 optimal weight: 10.0000 chunk 19 optimal weight: 0.0470 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 329 optimal weight: 9.9990 chunk 334 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 336 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 311 GLN B 471 GLN B 610 GLN C 204 HIS C 471 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.169710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.129356 restraints weight = 39451.542| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.06 r_work: 0.3315 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30681 Z= 0.107 Angle : 0.519 10.897 41796 Z= 0.262 Chirality : 0.043 0.179 4830 Planarity : 0.004 0.054 5295 Dihedral : 4.310 52.764 4040 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.44 % Allowed : 15.36 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.18 (0.14), residues: 3699 helix: 2.26 (0.21), residues: 666 sheet: 0.40 (0.16), residues: 960 loop : -0.74 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 234 TYR 0.015 0.001 TYR B1064 PHE 0.039 0.001 PHE B 130 TRP 0.064 0.002 TRP H 36 HIS 0.003 0.000 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (30588) covalent geometry : angle 0.51147 / 0.26 (41562) SS BOND : bond 0.00215 / 0.13 ( 45) SS BOND : angle 0.96716 / 0.69 ( 90) hydrogen bonds : bond 0.03626 / 2.33 ( 1221) hydrogen bonds : angle 4.93612 / 3.37 ( 3261) link_BETA1-4 : bond 0.00353 / 0.21 ( 12) link_BETA1-4 : angle 0.84356 / 0.54 ( 36) link_NAG-ASN : bond 0.00240 / 0.14 ( 36) link_NAG-ASN : angle 1.63751 / 1.05 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10020.32 seconds wall clock time: 171 minutes 32.52 seconds (10292.52 seconds total)