Starting phenix.real_space_refine on Tue May 27 22:37:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cim_16678/05_2025/8cim_16678.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cim_16678/05_2025/8cim_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cim_16678/05_2025/8cim_16678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cim_16678/05_2025/8cim_16678.map" model { file = "/net/cci-nas-00/data/ceres_data/8cim_16678/05_2025/8cim_16678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cim_16678/05_2025/8cim_16678.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 24 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 dihedrals: 24 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 16.57, per 1000 atoms: 0.55 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: 7.14 Conformation dependent library (CDL) restraints added in 3.7 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: 4.66 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: 14.94 Time building geometry restraints manager: 8.20 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: 17881 18.00 - 35.99: 751 35.99 - 53.99: 132 53.99 - 71.99: 22 71.99 - 89.98: 9 Dihedral angle restraints: 18795 sinusoidal: 7902 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 18792 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: 0.00 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.870 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: 1.310 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 70.020 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 10.290 89.984 11670 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP B 433 HIS 0.004 0.001 HIS C1061 PHE 0.014 0.001 PHE B 374 TYR 0.018 0.001 TYR A 492 ARG 0.003 0.000 ARG B 400 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 36) link_NAG-ASN : angle 1.83719 ( 108) link_BETA1-4 : bond 0.00256 ( 12) link_BETA1-4 : angle 0.95540 ( 36) hydrogen bonds : bond 0.13830 ( 1221) hydrogen bonds : angle 6.80738 ( 3261) SS BOND : bond 0.00289 ( 45) SS BOND : angle 0.73324 ( 90) covalent geometry : bond 0.00431 (30588) covalent geometry : angle 0.53985 (41562) *********************** 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 : 3.296 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: 0.7681 (m-30) REVERT: A 340 ASN cc_start: 0.7722 (t0) cc_final: 0.7456 (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: 0.6682 (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: 0.7497 (m-30) REVERT: B 340 ASN cc_start: 0.7707 (t0) cc_final: 0.7020 (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: 0.7380 (tp-100) REVERT: C 336 ASP cc_start: 0.7979 (m-30) cc_final: 0.7684 (m-30) REVERT: C 340 ASN cc_start: 0.7727 (t0) cc_final: 0.7326 (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: 0.7585 (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: 0.5583 (m-10) outliers start: 31 outliers final: 15 residues processed: 522 average time/residue: 1.2203 time to fit residues: 762.7680 Evaluate side-chains 294 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 277 time to evaluate : 2.965 ------------------------------------------------------------------------------- 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 314 optimal weight: 10.0000 chunk 281 optimal weight: 0.4980 chunk 156 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 291 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 337 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 GLN B 84 ASN B 414 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.173820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130175 restraints weight = 40020.035| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.77 r_work: 0.3322 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30681 Z= 0.146 Angle : 0.559 9.403 41796 Z= 0.286 Chirality : 0.045 0.242 4830 Planarity : 0.004 0.049 5295 Dihedral : 6.235 122.575 5063 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.15 % Allowed : 9.89 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3699 helix: 1.96 (0.20), residues: 687 sheet: 0.07 (0.16), residues: 1005 loop : -0.59 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 36 HIS 0.005 0.001 HIS E 55 PHE 0.014 0.001 PHE E 71 TYR 0.018 0.001 TYR A 753 ARG 0.005 0.000 ARG C 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 36) link_NAG-ASN : angle 2.08687 ( 108) link_BETA1-4 : bond 0.00368 ( 12) link_BETA1-4 : angle 0.89501 ( 36) hydrogen bonds : bond 0.04339 ( 1221) hydrogen bonds : angle 5.44524 ( 3261) SS BOND : bond 0.00398 ( 45) SS BOND : angle 1.77455 ( 90) covalent geometry : bond 0.00346 (30588) covalent geometry : angle 0.54385 (41562) *********************** 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 366 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 296 time to evaluate : 3.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7117 (OUTLIER) cc_final: 0.6901 (p) REVERT: A 50 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8001 (t70) REVERT: A 87 VAL cc_start: 0.8841 (t) cc_final: 0.8599 (p) REVERT: A 336 ASP cc_start: 0.8099 (m-30) cc_final: 0.7795 (m-30) REVERT: A 340 ASN cc_start: 0.7801 (t0) cc_final: 0.7309 (p0) REVERT: A 354 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8309 (ttp80) REVERT: A 513 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6464 (tt0) REVERT: A 526 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7751 (mptt) REVERT: A 1014 GLU cc_start: 0.8463 (tt0) cc_final: 0.8244 (tt0) REVERT: B 26 THR cc_start: 0.7116 (OUTLIER) cc_final: 0.6808 (p) REVERT: B 81 LEU cc_start: 0.7474 (mm) cc_final: 0.7212 (mp) REVERT: B 87 VAL cc_start: 0.8861 (t) cc_final: 0.8595 (p) REVERT: B 311 GLN cc_start: 0.8233 (tt0) cc_final: 0.8004 (tp-100) REVERT: B 336 ASP cc_start: 0.8069 (m-30) cc_final: 0.7780 (m-30) REVERT: B 340 ASN cc_start: 0.7853 (t0) cc_final: 0.7316 (p0) REVERT: B 354 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8349 (ttp80) REVERT: B 513 GLU cc_start: 0.7487 (tt0) cc_final: 0.7245 (tt0) REVERT: B 526 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7689 (mptt) REVERT: B 773 LYS cc_start: 0.8873 (tttt) cc_final: 0.8623 (tttm) REVERT: B 897 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8286 (mtp) REVERT: B 1014 GLU cc_start: 0.8514 (tt0) cc_final: 0.8271 (tt0) REVERT: C 26 THR cc_start: 0.7176 (OUTLIER) cc_final: 0.6938 (p) REVERT: C 50 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.7980 (t70) REVERT: C 81 LEU cc_start: 0.7526 (mm) cc_final: 0.7249 (mp) REVERT: C 87 VAL cc_start: 0.8848 (t) cc_final: 0.8595 (p) REVERT: C 197 TYR cc_start: 0.7036 (m-80) cc_final: 0.6623 (m-80) REVERT: C 234 ARG cc_start: 0.7985 (mtt90) cc_final: 0.7711 (mtm-85) REVERT: C 336 ASP cc_start: 0.8071 (m-30) cc_final: 0.7781 (m-30) REVERT: C 340 ASN cc_start: 0.7799 (t0) cc_final: 0.7358 (p0) REVERT: C 354 ARG cc_start: 0.8623 (ttp80) cc_final: 0.8260 (ttp80) REVERT: C 463 ARG cc_start: 0.8440 (ttm110) cc_final: 0.8234 (ttm170) REVERT: C 513 GLU cc_start: 0.7465 (tt0) cc_final: 0.7172 (tt0) REVERT: C 526 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7781 (mptt) REVERT: C 1014 GLU cc_start: 0.8598 (tt0) cc_final: 0.8344 (tt0) REVERT: C 1135 TYR cc_start: 0.8118 (t80) cc_final: 0.7875 (t80) REVERT: D 80 TYR cc_start: 0.7411 (m-10) cc_final: 0.7156 (m-10) REVERT: F 81 MET cc_start: 0.8278 (ttp) cc_final: 0.7901 (tmm) REVERT: G 37 GLN cc_start: 0.6488 (tt0) cc_final: 0.5996 (pp30) REVERT: H 64 PHE cc_start: 0.6476 (m-80) cc_final: 0.5525 (m-10) REVERT: L 33 LEU cc_start: 0.7675 (tp) cc_final: 0.7338 (tp) REVERT: L 47 LEU cc_start: 0.7517 (mt) cc_final: 0.7279 (mp) outliers start: 70 outliers final: 36 residues processed: 349 average time/residue: 1.1012 time to fit residues: 470.1102 Evaluate side-chains 298 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 256 time to evaluate : 3.199 ------------------------------------------------------------------------------- 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 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 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 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 121 optimal weight: 0.0570 chunk 130 optimal weight: 0.9980 chunk 332 optimal weight: 9.9990 chunk 367 optimal weight: 20.0000 chunk 166 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 326 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 932 GLN ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 GLN B 962 GLN D 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.168501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.127092 restraints weight = 39778.256| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.46 r_work: 0.3302 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30681 Z= 0.156 Angle : 0.537 8.911 41796 Z= 0.275 Chirality : 0.045 0.227 4830 Planarity : 0.004 0.055 5295 Dihedral : 5.359 49.551 5050 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.33 % Allowed : 11.24 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3699 helix: 2.13 (0.21), residues: 666 sheet: 0.17 (0.17), residues: 942 loop : -0.66 (0.14), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 36 HIS 0.003 0.001 HIS C1061 PHE 0.013 0.001 PHE D 29 TYR 0.017 0.001 TYR C1064 ARG 0.004 0.000 ARG A 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 36) link_NAG-ASN : angle 1.92681 ( 108) link_BETA1-4 : bond 0.00317 ( 12) link_BETA1-4 : angle 0.94735 ( 36) hydrogen bonds : bond 0.04167 ( 1221) hydrogen bonds : angle 5.23856 ( 3261) SS BOND : bond 0.00330 ( 45) SS BOND : angle 1.37278 ( 90) covalent geometry : bond 0.00376 (30588) covalent geometry : angle 0.52494 (41562) *********************** 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: 76 poor density : 275 time to evaluate : 3.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7071 (OUTLIER) cc_final: 0.6839 (p) REVERT: A 50 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8110 (t70) REVERT: A 87 VAL cc_start: 0.8842 (t) cc_final: 0.8589 (p) REVERT: A 336 ASP cc_start: 0.8054 (m-30) cc_final: 0.7784 (m-30) REVERT: A 340 ASN cc_start: 0.7844 (t0) cc_final: 0.7305 (p0) REVERT: A 354 ARG cc_start: 0.8639 (ttp80) cc_final: 0.8246 (ttp80) REVERT: A 513 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6378 (tt0) REVERT: A 526 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7770 (mptt) REVERT: A 1014 GLU cc_start: 0.8501 (tt0) cc_final: 0.8277 (tt0) REVERT: B 26 THR cc_start: 0.7009 (OUTLIER) cc_final: 0.6681 (p) REVERT: B 81 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7235 (mp) REVERT: B 87 VAL cc_start: 0.8858 (t) cc_final: 0.8580 (p) REVERT: B 311 GLN cc_start: 0.8171 (tt0) cc_final: 0.7969 (tp-100) REVERT: B 336 ASP cc_start: 0.8081 (m-30) cc_final: 0.7784 (m-30) REVERT: B 340 ASN cc_start: 0.7871 (t0) cc_final: 0.7305 (p0) REVERT: B 354 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8341 (ttp80) REVERT: B 526 LYS cc_start: 0.8358 (mmtt) cc_final: 0.7744 (mptt) REVERT: B 851 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8046 (tttm) REVERT: B 1014 GLU cc_start: 0.8551 (tt0) cc_final: 0.8263 (tt0) REVERT: C 26 THR cc_start: 0.7119 (OUTLIER) cc_final: 0.6878 (p) REVERT: C 81 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7287 (mp) REVERT: C 87 VAL cc_start: 0.8877 (t) cc_final: 0.8593 (p) REVERT: C 197 TYR cc_start: 0.7048 (m-80) cc_final: 0.6523 (m-10) REVERT: C 234 ARG cc_start: 0.8033 (mtt90) cc_final: 0.7758 (mtm-85) REVERT: C 336 ASP cc_start: 0.8086 (m-30) cc_final: 0.7825 (m-30) REVERT: C 340 ASN cc_start: 0.7779 (t0) cc_final: 0.7314 (p0) REVERT: C 354 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8237 (ttp80) REVERT: C 526 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7781 (mptt) REVERT: C 793 TYR cc_start: 0.6796 (t80) cc_final: 0.6513 (t80) REVERT: C 1014 GLU cc_start: 0.8642 (tt0) cc_final: 0.8376 (tt0) REVERT: C 1135 TYR cc_start: 0.8156 (t80) cc_final: 0.7853 (t80) REVERT: G 37 GLN cc_start: 0.6365 (tt0) cc_final: 0.5902 (pp30) REVERT: H 64 PHE cc_start: 0.6502 (m-80) cc_final: 0.5541 (m-10) REVERT: L 33 LEU cc_start: 0.7798 (tp) cc_final: 0.7486 (tp) outliers start: 76 outliers final: 39 residues processed: 332 average time/residue: 1.0267 time to fit residues: 425.7654 Evaluate side-chains 299 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 3.124 ------------------------------------------------------------------------------- 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 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 805 ASP Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 934 SER 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 22 THR 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 183 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 295 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 224 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 339 optimal weight: 10.0000 chunk 357 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 303 optimal weight: 0.8980 chunk 337 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 932 GLN A1122 ASN B 471 GLN B 801 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 = 0.4108 r_free = 0.4108 target = 0.168355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.128005 restraints weight = 39750.714| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.04 r_work: 0.3287 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30681 Z= 0.178 Angle : 0.552 10.187 41796 Z= 0.281 Chirality : 0.045 0.222 4830 Planarity : 0.004 0.049 5295 Dihedral : 5.194 50.715 5050 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.92 % Allowed : 11.80 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3699 helix: 2.04 (0.20), residues: 666 sheet: 0.26 (0.16), residues: 942 loop : -0.76 (0.14), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 35 HIS 0.004 0.001 HIS C1061 PHE 0.016 0.001 PHE D 29 TYR 0.017 0.001 TYR A1064 ARG 0.004 0.000 ARG A 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 36) link_NAG-ASN : angle 1.96673 ( 108) link_BETA1-4 : bond 0.00254 ( 12) link_BETA1-4 : angle 0.93895 ( 36) hydrogen bonds : bond 0.04251 ( 1221) hydrogen bonds : angle 5.16738 ( 3261) SS BOND : bond 0.00276 ( 45) SS BOND : angle 1.27264 ( 90) covalent geometry : bond 0.00433 (30588) covalent geometry : angle 0.54015 (41562) *********************** 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 363 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 268 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7075 (OUTLIER) cc_final: 0.6865 (p) REVERT: A 50 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8178 (t70) REVERT: A 87 VAL cc_start: 0.8854 (t) cc_final: 0.8622 (p) REVERT: A 197 TYR cc_start: 0.7195 (m-80) cc_final: 0.6836 (m-80) REVERT: A 336 ASP cc_start: 0.8069 (m-30) cc_final: 0.7809 (m-30) REVERT: A 340 ASN cc_start: 0.7906 (t0) cc_final: 0.7315 (p0) REVERT: A 354 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8240 (ttp80) REVERT: A 513 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6513 (tt0) REVERT: A 526 LYS cc_start: 0.8333 (mmtt) cc_final: 0.7794 (mptt) REVERT: A 1014 GLU cc_start: 0.8526 (tt0) cc_final: 0.8317 (tt0) REVERT: B 26 THR cc_start: 0.7026 (OUTLIER) cc_final: 0.6671 (p) REVERT: B 27 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7997 (t0) REVERT: B 81 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7230 (mp) REVERT: B 87 VAL cc_start: 0.8879 (t) cc_final: 0.8590 (p) REVERT: B 234 ARG cc_start: 0.8090 (mtt90) cc_final: 0.7814 (mtm-85) REVERT: B 336 ASP cc_start: 0.8117 (m-30) cc_final: 0.7857 (m-30) REVERT: B 340 ASN cc_start: 0.7834 (t0) cc_final: 0.7278 (p0) REVERT: B 354 ARG cc_start: 0.8653 (ttp80) cc_final: 0.8331 (ttp80) REVERT: B 483 PHE cc_start: 0.8119 (t80) cc_final: 0.7850 (t80) REVERT: B 513 GLU cc_start: 0.7519 (tt0) cc_final: 0.6025 (tt0) REVERT: B 526 LYS cc_start: 0.8377 (mmtt) cc_final: 0.7815 (mptt) REVERT: B 851 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8067 (tttm) REVERT: B 974 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8423 (mp) REVERT: B 1014 GLU cc_start: 0.8579 (tt0) cc_final: 0.8286 (tt0) REVERT: C 26 THR cc_start: 0.7109 (OUTLIER) cc_final: 0.6878 (p) REVERT: C 81 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7259 (mp) REVERT: C 87 VAL cc_start: 0.8905 (t) cc_final: 0.8629 (p) REVERT: C 197 TYR cc_start: 0.7097 (m-80) cc_final: 0.6589 (m-10) REVERT: C 234 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7786 (mtm-85) REVERT: C 336 ASP cc_start: 0.8074 (m-30) cc_final: 0.7805 (m-30) REVERT: C 340 ASN cc_start: 0.7785 (t0) cc_final: 0.7291 (p0) REVERT: C 354 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8218 (ttp80) REVERT: C 513 GLU cc_start: 0.7590 (tt0) cc_final: 0.7383 (tt0) REVERT: C 526 LYS cc_start: 0.8344 (mmtt) cc_final: 0.7806 (mptt) REVERT: C 961 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8650 (mttt) REVERT: C 1014 GLU cc_start: 0.8650 (tt0) cc_final: 0.8373 (tt0) REVERT: C 1135 TYR cc_start: 0.8199 (t80) cc_final: 0.7942 (t80) REVERT: G 24 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7555 (ttt-90) REVERT: G 37 GLN cc_start: 0.6459 (tt0) cc_final: 0.5950 (pp30) REVERT: H 23 LYS cc_start: 0.8009 (tttm) cc_final: 0.7542 (ttmt) REVERT: H 48 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7017 (mtp) REVERT: H 64 PHE cc_start: 0.6461 (m-80) cc_final: 0.5517 (m-10) outliers start: 95 outliers final: 47 residues processed: 341 average time/residue: 1.0750 time to fit residues: 450.8143 Evaluate side-chains 312 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 253 time to evaluate : 3.071 ------------------------------------------------------------------------------- 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 128 CYS 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 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 27 ASN 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 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 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 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 961 LYS 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 F residue 35 SER 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 99 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 264 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 335 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN A 932 GLN B 311 GLN B 402 ASN C 204 HIS C 311 GLN C 402 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 = 0.4131 r_free = 0.4131 target = 0.170577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.130792 restraints weight = 39547.959| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.92 r_work: 0.3369 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1985 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= 0.109 Angle : 0.504 9.223 41796 Z= 0.256 Chirality : 0.043 0.201 4830 Planarity : 0.004 0.049 5295 Dihedral : 4.848 50.303 5050 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.30 % Allowed : 12.93 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3699 helix: 2.51 (0.21), residues: 645 sheet: 0.41 (0.17), residues: 903 loop : -0.67 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 35 HIS 0.003 0.000 HIS C 204 PHE 0.015 0.001 PHE D 29 TYR 0.015 0.001 TYR B1064 ARG 0.007 0.000 ARG A 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 36) link_NAG-ASN : angle 1.81501 ( 108) link_BETA1-4 : bond 0.00312 ( 12) link_BETA1-4 : angle 0.83222 ( 36) hydrogen bonds : bond 0.03657 ( 1221) hydrogen bonds : angle 4.99309 ( 3261) SS BOND : bond 0.00211 ( 45) SS BOND : angle 0.98704 ( 90) covalent geometry : bond 0.00252 (30588) covalent geometry : angle 0.49443 (41562) *********************** 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 359 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 284 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 VAL cc_start: 0.8805 (t) cc_final: 0.8574 (p) REVERT: A 336 ASP cc_start: 0.8031 (m-30) cc_final: 0.7759 (m-30) REVERT: A 340 ASN cc_start: 0.7838 (t0) cc_final: 0.7275 (p0) REVERT: A 354 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8228 (ttp80) REVERT: A 483 PHE cc_start: 0.8158 (t80) cc_final: 0.7901 (t80) REVERT: A 513 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6280 (tt0) REVERT: A 526 LYS cc_start: 0.8330 (mmtt) cc_final: 0.7802 (mptt) REVERT: A 793 TYR cc_start: 0.6861 (t80) cc_final: 0.6565 (t80) REVERT: A 1014 GLU cc_start: 0.8435 (tt0) cc_final: 0.8226 (tt0) REVERT: B 26 THR cc_start: 0.6980 (OUTLIER) cc_final: 0.6621 (p) REVERT: B 81 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7299 (mp) REVERT: B 87 VAL cc_start: 0.8817 (t) cc_final: 0.8543 (p) REVERT: B 336 ASP cc_start: 0.8057 (m-30) cc_final: 0.7763 (m-30) REVERT: B 340 ASN cc_start: 0.7767 (t0) cc_final: 0.7232 (p0) REVERT: B 354 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8310 (ttp80) REVERT: B 463 ARG cc_start: 0.8344 (ttm110) cc_final: 0.8012 (ttm170) REVERT: B 513 GLU cc_start: 0.7449 (tt0) cc_final: 0.7215 (tt0) REVERT: B 526 LYS cc_start: 0.8363 (mmtt) cc_final: 0.7810 (mptt) REVERT: B 793 TYR cc_start: 0.6828 (t80) cc_final: 0.6599 (t80) REVERT: B 995 THR cc_start: 0.8763 (m) cc_final: 0.8491 (p) REVERT: B 1014 GLU cc_start: 0.8509 (tt0) cc_final: 0.8281 (tt0) REVERT: C 26 THR cc_start: 0.7116 (OUTLIER) cc_final: 0.6898 (p) REVERT: C 81 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7270 (mp) REVERT: C 87 VAL cc_start: 0.8823 (t) cc_final: 0.8569 (p) REVERT: C 197 TYR cc_start: 0.7061 (m-80) cc_final: 0.6479 (m-10) REVERT: C 336 ASP cc_start: 0.8055 (m-30) cc_final: 0.7797 (m-30) REVERT: C 340 ASN cc_start: 0.7719 (t0) cc_final: 0.7251 (p0) REVERT: C 526 LYS cc_start: 0.8355 (mmtt) cc_final: 0.7805 (mptt) REVERT: C 793 TYR cc_start: 0.6852 (t80) cc_final: 0.6599 (t80) REVERT: C 1014 GLU cc_start: 0.8564 (tt0) cc_final: 0.8323 (tt0) REVERT: C 1135 TYR cc_start: 0.8174 (t80) cc_final: 0.7893 (t80) REVERT: G 24 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7546 (ttt-90) REVERT: G 37 GLN cc_start: 0.6466 (tt0) cc_final: 0.5957 (pp30) REVERT: H 23 LYS cc_start: 0.7979 (tttm) cc_final: 0.7537 (ttmt) REVERT: H 48 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7035 (mtp) REVERT: H 64 PHE cc_start: 0.6433 (m-80) cc_final: 0.5560 (m-10) REVERT: L 33 LEU cc_start: 0.7648 (mt) cc_final: 0.7415 (tp) outliers start: 75 outliers final: 40 residues processed: 330 average time/residue: 1.0907 time to fit residues: 443.0672 Evaluate side-chains 309 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 480 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 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 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 960 VAL Chi-restraints excluded: chain B residue 1078 ILE 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 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 102 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 67 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 chunk 252 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 287 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 315 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 344 optimal weight: 2.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN A 516 HIS A 932 GLN B 131 GLN B 351 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN B 516 HIS B 801 GLN B 932 GLN C 204 HIS ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 HIS C 700 ASN C 962 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.160711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.119469 restraints weight = 38850.699| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.11 r_work: 0.3156 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 30681 Z= 0.273 Angle : 0.633 10.890 41796 Z= 0.323 Chirality : 0.049 0.243 4830 Planarity : 0.004 0.066 5295 Dihedral : 5.557 58.556 5049 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.95 % Allowed : 13.30 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3699 helix: 1.73 (0.20), residues: 666 sheet: 0.24 (0.16), residues: 960 loop : -0.92 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP H 36 HIS 0.005 0.001 HIS C1061 PHE 0.026 0.002 PHE A 130 TYR 0.019 0.002 TYR A1064 ARG 0.007 0.001 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 36) link_NAG-ASN : angle 2.28768 ( 108) link_BETA1-4 : bond 0.00206 ( 12) link_BETA1-4 : angle 1.11283 ( 36) hydrogen bonds : bond 0.04988 ( 1221) hydrogen bonds : angle 5.29806 ( 3261) SS BOND : bond 0.00375 ( 45) SS BOND : angle 1.41940 ( 90) covalent geometry : bond 0.00673 (30588) covalent geometry : angle 0.61947 (41562) *********************** 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 366 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 270 time to evaluate : 2.951 Fit side-chains revert: symmetry clash REVERT: A 197 TYR cc_start: 0.7269 (m-80) cc_final: 0.6897 (m-80) REVERT: A 336 ASP cc_start: 0.8154 (m-30) cc_final: 0.7953 (m-30) REVERT: A 340 ASN cc_start: 0.7903 (t0) cc_final: 0.7357 (p0) REVERT: A 354 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8199 (ttp80) REVERT: A 475 LYS cc_start: 0.7903 (pmmt) cc_final: 0.6716 (pptt) REVERT: A 513 GLU cc_start: 0.7666 (mt-10) cc_final: 0.6593 (tt0) REVERT: A 526 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7856 (mptt) REVERT: A 1014 GLU cc_start: 0.8677 (tt0) cc_final: 0.8477 (tt0) REVERT: B 26 THR cc_start: 0.6935 (OUTLIER) cc_final: 0.6556 (p) REVERT: B 87 VAL cc_start: 0.8885 (t) cc_final: 0.8629 (p) REVERT: B 336 ASP cc_start: 0.8156 (m-30) cc_final: 0.7942 (m-30) REVERT: B 340 ASN cc_start: 0.7842 (t0) cc_final: 0.7359 (p0) REVERT: B 354 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8271 (ttp80) REVERT: B 513 GLU cc_start: 0.7706 (tt0) cc_final: 0.6608 (tt0) REVERT: B 526 LYS cc_start: 0.8404 (mmtt) cc_final: 0.7891 (mptt) REVERT: B 851 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8174 (tttm) REVERT: B 974 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8436 (mp) REVERT: B 1014 GLU cc_start: 0.8719 (tt0) cc_final: 0.8473 (tt0) REVERT: C 26 THR cc_start: 0.7224 (OUTLIER) cc_final: 0.7010 (p) REVERT: C 87 VAL cc_start: 0.8944 (t) cc_final: 0.8684 (p) REVERT: C 197 TYR cc_start: 0.7174 (m-80) cc_final: 0.6615 (m-10) REVERT: C 234 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7908 (mtm-85) REVERT: C 316 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7659 (mtt-85) REVERT: C 336 ASP cc_start: 0.8147 (m-30) cc_final: 0.7946 (m-30) REVERT: C 340 ASN cc_start: 0.7802 (t0) cc_final: 0.7369 (p0) REVERT: C 526 LYS cc_start: 0.8366 (mmtt) cc_final: 0.7842 (mptt) REVERT: C 961 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8757 (mttt) REVERT: C 1014 GLU cc_start: 0.8760 (tt0) cc_final: 0.8514 (tt0) REVERT: G 24 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7515 (ttt-90) REVERT: G 37 GLN cc_start: 0.6744 (tt0) cc_final: 0.6090 (pp30) REVERT: H 23 LYS cc_start: 0.8040 (tttm) cc_final: 0.7642 (ttmt) REVERT: H 29 PHE cc_start: 0.7474 (t80) cc_final: 0.7107 (t80) REVERT: H 48 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7148 (mtp) REVERT: H 64 PHE cc_start: 0.6290 (m-80) cc_final: 0.5569 (m-10) outliers start: 96 outliers final: 55 residues processed: 341 average time/residue: 1.0638 time to fit residues: 446.8677 Evaluate side-chains 306 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 243 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR 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 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 672 GLN 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 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 1133 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 50 ASP 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 961 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1091 VAL 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 35 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 25 optimal weight: 0.8980 chunk 225 optimal weight: 0.8980 chunk 366 optimal weight: 0.6980 chunk 223 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 281 optimal weight: 0.7980 chunk 285 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 236 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** G 38 GLN ** 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 = 0.4010 r_free = 0.4010 target = 0.163861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.123396 restraints weight = 38491.508| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.93 r_work: 0.3221 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30681 Z= 0.121 Angle : 0.534 11.239 41796 Z= 0.272 Chirality : 0.044 0.174 4830 Planarity : 0.004 0.059 5295 Dihedral : 5.230 58.531 5049 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.27 % Allowed : 14.35 % Favored : 83.38 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3699 helix: 2.08 (0.21), residues: 666 sheet: 0.29 (0.16), residues: 951 loop : -0.82 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 36 HIS 0.004 0.001 HIS C 204 PHE 0.027 0.001 PHE A 165 TYR 0.016 0.001 TYR B1064 ARG 0.005 0.000 ARG B 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 36) link_NAG-ASN : angle 2.35172 ( 108) link_BETA1-4 : bond 0.00331 ( 12) link_BETA1-4 : angle 0.85251 ( 36) hydrogen bonds : bond 0.03848 ( 1221) hydrogen bonds : angle 5.07087 ( 3261) SS BOND : bond 0.00245 ( 45) SS BOND : angle 1.14930 ( 90) covalent geometry : bond 0.00281 (30588) covalent geometry : angle 0.51890 (41562) *********************** 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 340 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 266 time to evaluate : 3.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8100 (t70) REVERT: A 340 ASN cc_start: 0.7532 (t0) cc_final: 0.7242 (p0) REVERT: A 475 LYS cc_start: 0.7926 (pmmt) cc_final: 0.6759 (pptt) REVERT: A 513 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6358 (tt0) REVERT: A 526 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7766 (mptt) REVERT: A 793 TYR cc_start: 0.6950 (t80) cc_final: 0.6674 (t80) REVERT: B 26 THR cc_start: 0.6834 (OUTLIER) cc_final: 0.6514 (p) REVERT: B 81 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7417 (mp) REVERT: B 87 VAL cc_start: 0.8757 (t) cc_final: 0.8495 (p) REVERT: B 340 ASN cc_start: 0.7464 (t0) cc_final: 0.7254 (p0) REVERT: B 463 ARG cc_start: 0.8156 (ttm110) cc_final: 0.7873 (ttm170) REVERT: B 526 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7772 (mptt) REVERT: B 1014 GLU cc_start: 0.8350 (tt0) cc_final: 0.8133 (tt0) REVERT: C 50 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8066 (t70) REVERT: C 81 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7290 (mp) REVERT: C 87 VAL cc_start: 0.8789 (t) cc_final: 0.8523 (p) REVERT: C 197 TYR cc_start: 0.6928 (m-80) cc_final: 0.6395 (m-10) REVERT: C 475 LYS cc_start: 0.7310 (pptt) cc_final: 0.7077 (pmmt) REVERT: C 526 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7742 (mptt) REVERT: C 793 TYR cc_start: 0.6830 (t80) cc_final: 0.6629 (t80) REVERT: G 24 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7456 (ttt-90) REVERT: G 37 GLN cc_start: 0.6776 (tt0) cc_final: 0.6143 (pp30) REVERT: H 23 LYS cc_start: 0.7964 (tttm) cc_final: 0.7572 (ttmt) REVERT: H 48 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7128 (mtp) REVERT: H 64 PHE cc_start: 0.6252 (m-80) cc_final: 0.5591 (m-10) outliers start: 74 outliers final: 44 residues processed: 318 average time/residue: 1.0982 time to fit residues: 433.1424 Evaluate side-chains 299 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 248 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 105 THR 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 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 500 VAL 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 1078 ILE Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1103 GLN 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 9 optimal weight: 8.9990 chunk 353 optimal weight: 10.0000 chunk 323 optimal weight: 20.0000 chunk 117 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 208 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 GLN A 932 GLN B 471 GLN C 204 HIS ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.167580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126451 restraints weight = 39604.466| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.34 r_work: 0.3276 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30681 Z= 0.140 Angle : 0.540 11.274 41796 Z= 0.274 Chirality : 0.044 0.194 4830 Planarity : 0.004 0.054 5295 Dihedral : 5.060 55.084 5048 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.27 % Allowed : 14.72 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3699 helix: 2.11 (0.21), residues: 666 sheet: 0.31 (0.16), residues: 978 loop : -0.83 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP G 35 HIS 0.004 0.001 HIS C 204 PHE 0.032 0.001 PHE A 130 TYR 0.016 0.001 TYR B1064 ARG 0.010 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 36) link_NAG-ASN : angle 2.06854 ( 108) link_BETA1-4 : bond 0.00332 ( 12) link_BETA1-4 : angle 0.97522 ( 36) hydrogen bonds : bond 0.03930 ( 1221) hydrogen bonds : angle 5.02703 ( 3261) SS BOND : bond 0.00234 ( 45) SS BOND : angle 1.09799 ( 90) covalent geometry : bond 0.00337 (30588) covalent geometry : angle 0.52757 (41562) *********************** 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 322 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 248 time to evaluate : 3.235 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8167 (t70) REVERT: A 197 TYR cc_start: 0.7201 (m-80) cc_final: 0.6612 (m-80) REVERT: A 340 ASN cc_start: 0.7874 (t0) cc_final: 0.7228 (p0) REVERT: A 513 GLU cc_start: 0.7513 (mt-10) cc_final: 0.6428 (tt0) REVERT: A 526 LYS cc_start: 0.8408 (mmtt) cc_final: 0.7829 (mptt) REVERT: A 793 TYR cc_start: 0.6966 (t80) cc_final: 0.6634 (t80) REVERT: B 26 THR cc_start: 0.6824 (OUTLIER) cc_final: 0.6383 (p) REVERT: B 81 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7338 (mp) REVERT: B 87 VAL cc_start: 0.8855 (t) cc_final: 0.8559 (p) REVERT: B 340 ASN cc_start: 0.7784 (t0) cc_final: 0.7170 (p0) REVERT: B 355 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8629 (mm) REVERT: B 513 GLU cc_start: 0.7774 (tt0) cc_final: 0.6798 (tt0) REVERT: B 526 LYS cc_start: 0.8455 (mmtt) cc_final: 0.7837 (mptt) REVERT: B 793 TYR cc_start: 0.6832 (t80) cc_final: 0.6601 (t80) REVERT: B 851 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8053 (tttm) REVERT: B 1014 GLU cc_start: 0.8550 (tt0) cc_final: 0.8263 (tt0) REVERT: C 50 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8155 (t70) REVERT: C 81 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7235 (mp) REVERT: C 87 VAL cc_start: 0.8879 (t) cc_final: 0.8581 (p) REVERT: C 197 TYR cc_start: 0.7127 (m-80) cc_final: 0.6529 (m-10) REVERT: C 228 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7358 (pp) REVERT: C 526 LYS cc_start: 0.8456 (mmtt) cc_final: 0.7831 (mptt) REVERT: C 793 TYR cc_start: 0.6851 (t80) cc_final: 0.6588 (t80) REVERT: G 24 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7594 (ttt-90) REVERT: G 37 GLN cc_start: 0.6600 (tt0) cc_final: 0.6024 (pp30) REVERT: H 23 LYS cc_start: 0.7977 (tttm) cc_final: 0.7505 (ttmt) REVERT: H 29 PHE cc_start: 0.7129 (t80) cc_final: 0.6810 (t80) REVERT: H 48 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7167 (mtp) REVERT: H 64 PHE cc_start: 0.6311 (m-80) cc_final: 0.5686 (m-10) outliers start: 74 outliers final: 44 residues processed: 303 average time/residue: 0.9974 time to fit residues: 374.5554 Evaluate side-chains 288 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 234 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 105 THR 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 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 336 ASP Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 500 VAL 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 1078 ILE Chi-restraints excluded: chain B residue 1088 ARG 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 330 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 471 GLN 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 124 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 253 optimal weight: 0.7980 chunk 361 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 932 GLN 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** H 101 HIS ** 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 = 0.3985 r_free = 0.3985 target = 0.161746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120908 restraints weight = 38666.828| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.01 r_work: 0.3182 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 30681 Z= 0.205 Angle : 0.579 10.411 41796 Z= 0.296 Chirality : 0.046 0.193 4830 Planarity : 0.004 0.055 5295 Dihedral : 5.165 56.917 5048 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.09 % Allowed : 15.36 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3699 helix: 1.93 (0.20), residues: 666 sheet: 0.27 (0.16), residues: 951 loop : -0.88 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 36 HIS 0.004 0.001 HIS L 92 PHE 0.024 0.002 PHE A 165 TYR 0.018 0.001 TYR A1064 ARG 0.009 0.000 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 36) link_NAG-ASN : angle 2.02002 ( 108) link_BETA1-4 : bond 0.00251 ( 12) link_BETA1-4 : angle 1.01253 ( 36) hydrogen bonds : bond 0.04411 ( 1221) hydrogen bonds : angle 5.15678 ( 3261) SS BOND : bond 0.00305 ( 45) SS BOND : angle 1.23989 ( 90) covalent geometry : bond 0.00504 (30588) covalent geometry : angle 0.56813 (41562) *********************** 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 313 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 245 time to evaluate : 3.053 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8258 (t70) REVERT: A 197 TYR cc_start: 0.7215 (m-80) cc_final: 0.6648 (m-80) REVERT: A 340 ASN cc_start: 0.7864 (t0) cc_final: 0.7315 (p0) REVERT: A 513 GLU cc_start: 0.7615 (mt-10) cc_final: 0.6597 (tt0) REVERT: A 526 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7852 (mptt) REVERT: B 26 THR cc_start: 0.6883 (OUTLIER) cc_final: 0.6513 (p) REVERT: B 81 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7469 (mp) REVERT: B 87 VAL cc_start: 0.8849 (t) cc_final: 0.8606 (p) REVERT: B 340 ASN cc_start: 0.7780 (t0) cc_final: 0.7283 (p0) REVERT: B 355 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8666 (mm) REVERT: B 513 GLU cc_start: 0.7814 (tt0) cc_final: 0.6826 (tt0) REVERT: B 526 LYS cc_start: 0.8395 (mmtt) cc_final: 0.7896 (mptt) REVERT: B 851 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8081 (tttm) REVERT: B 1014 GLU cc_start: 0.8700 (tt0) cc_final: 0.8453 (tt0) REVERT: C 81 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7377 (mp) REVERT: C 87 VAL cc_start: 0.8928 (t) cc_final: 0.8677 (p) REVERT: C 197 TYR cc_start: 0.7170 (m-80) cc_final: 0.6558 (m-10) REVERT: C 228 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7446 (pp) REVERT: C 484 ASN cc_start: 0.7978 (m-40) cc_final: 0.7772 (m-40) REVERT: C 526 LYS cc_start: 0.8381 (mmtt) cc_final: 0.7892 (mptt) REVERT: G 24 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7489 (ttt-90) REVERT: G 37 GLN cc_start: 0.6817 (tt0) cc_final: 0.6119 (pp30) REVERT: H 23 LYS cc_start: 0.8013 (tttm) cc_final: 0.7597 (ttmt) REVERT: H 29 PHE cc_start: 0.7214 (t80) cc_final: 0.6884 (t80) REVERT: H 48 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7239 (mtp) REVERT: H 64 PHE cc_start: 0.6132 (m-80) cc_final: 0.5651 (m-10) REVERT: L 32 TYR cc_start: 0.6725 (m-10) cc_final: 0.6525 (m-10) REVERT: L 33 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7834 (mm) outliers start: 68 outliers final: 48 residues processed: 296 average time/residue: 1.0778 time to fit residues: 399.2908 Evaluate side-chains 292 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 234 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 105 THR 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 336 ASP 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 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 355 ILE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 500 VAL 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 1078 ILE Chi-restraints excluded: chain B residue 1088 ARG 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 105 THR Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 228 ILE 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 1078 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1103 GLN 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 51 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU 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 256 optimal weight: 0.6980 chunk 364 optimal weight: 8.9990 chunk 263 optimal weight: 0.8980 chunk 198 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 276 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 279 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN A 932 GLN B 471 GLN C 204 HIS ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.168398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.127727 restraints weight = 39488.132| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.67 r_work: 0.3296 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30681 Z= 0.119 Angle : 0.531 11.503 41796 Z= 0.270 Chirality : 0.044 0.162 4830 Planarity : 0.004 0.069 5295 Dihedral : 4.876 57.620 5048 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.94 % Allowed : 15.61 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3699 helix: 2.15 (0.21), residues: 666 sheet: 0.28 (0.16), residues: 981 loop : -0.81 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP G 35 HIS 0.003 0.001 HIS C 204 PHE 0.032 0.001 PHE B 130 TYR 0.017 0.001 TYR C1135 ARG 0.009 0.000 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 36) link_NAG-ASN : angle 1.85423 ( 108) link_BETA1-4 : bond 0.00361 ( 12) link_BETA1-4 : angle 0.89478 ( 36) hydrogen bonds : bond 0.03793 ( 1221) hydrogen bonds : angle 5.01802 ( 3261) SS BOND : bond 0.00238 ( 45) SS BOND : angle 1.02835 ( 90) covalent geometry : bond 0.00281 (30588) covalent geometry : angle 0.52084 (41562) ********************** 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 315 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 252 time to evaluate : 3.064 Fit side-chains revert: symmetry clash REVERT: A 197 TYR cc_start: 0.7170 (m-80) cc_final: 0.6462 (m-80) REVERT: A 340 ASN cc_start: 0.7872 (t0) cc_final: 0.7258 (p0) REVERT: A 513 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6447 (tt0) REVERT: A 526 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7813 (mptt) REVERT: A 793 TYR cc_start: 0.6976 (t80) cc_final: 0.6695 (t80) REVERT: A 1089 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7213 (pp20) REVERT: B 26 THR cc_start: 0.6788 (OUTLIER) cc_final: 0.6364 (p) REVERT: B 81 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7364 (mp) REVERT: B 87 VAL cc_start: 0.8842 (t) cc_final: 0.8556 (p) REVERT: B 340 ASN cc_start: 0.7773 (t0) cc_final: 0.7199 (p0) REVERT: B 513 GLU cc_start: 0.7752 (tt0) cc_final: 0.6596 (tt0) REVERT: B 526 LYS cc_start: 0.8425 (mmtt) cc_final: 0.7840 (mptt) REVERT: B 793 TYR cc_start: 0.6891 (t80) cc_final: 0.6667 (t80) REVERT: B 851 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8090 (tttm) REVERT: B 1014 GLU cc_start: 0.8549 (tt0) cc_final: 0.8273 (tt0) REVERT: C 50 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8161 (t70) REVERT: C 81 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7277 (mp) REVERT: C 87 VAL cc_start: 0.8893 (t) cc_final: 0.8607 (p) REVERT: C 197 TYR cc_start: 0.7116 (m-80) cc_final: 0.6531 (m-10) REVERT: C 228 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7378 (pp) REVERT: C 526 LYS cc_start: 0.8457 (mmtt) cc_final: 0.7873 (mptt) REVERT: C 793 TYR cc_start: 0.6920 (t80) cc_final: 0.6677 (t80) REVERT: G 24 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7619 (ttt-90) REVERT: G 37 GLN cc_start: 0.6640 (tt0) cc_final: 0.6034 (pp30) REVERT: H 23 LYS cc_start: 0.7978 (tttm) cc_final: 0.7476 (ttmt) REVERT: H 29 PHE cc_start: 0.7075 (t80) cc_final: 0.6825 (t80) REVERT: H 48 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7159 (mtp) REVERT: H 64 PHE cc_start: 0.6195 (m-80) cc_final: 0.5734 (m-80) outliers start: 63 outliers final: 46 residues processed: 300 average time/residue: 0.9613 time to fit residues: 359.2332 Evaluate side-chains 298 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 243 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR 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 1078 ILE Chi-restraints excluded: chain A residue 1089 GLU 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 105 THR 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 500 VAL 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 1078 ILE Chi-restraints excluded: chain B residue 1088 ARG 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 105 THR Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 228 ILE 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 500 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 0.7980 chunk 279 optimal weight: 0.9980 chunk 265 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 234 optimal weight: 0.7980 chunk 185 optimal weight: 0.6980 chunk 275 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 274 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN A 471 GLN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.168913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127855 restraints weight = 39479.002| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.34 r_work: 0.3304 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2586 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= 0.114 Angle : 0.523 10.199 41796 Z= 0.266 Chirality : 0.044 0.163 4830 Planarity : 0.004 0.064 5295 Dihedral : 4.716 57.450 5048 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.15 % Allowed : 15.45 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3699 helix: 2.21 (0.21), residues: 666 sheet: 0.31 (0.16), residues: 981 loop : -0.77 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP G 35 HIS 0.004 0.001 HIS L 92 PHE 0.029 0.001 PHE A 165 TYR 0.018 0.001 TYR L 32 ARG 0.009 0.000 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 36) link_NAG-ASN : angle 1.81667 ( 108) link_BETA1-4 : bond 0.00378 ( 12) link_BETA1-4 : angle 0.96713 ( 36) hydrogen bonds : bond 0.03692 ( 1221) hydrogen bonds : angle 4.95649 ( 3261) SS BOND : bond 0.00242 ( 45) SS BOND : angle 0.97599 ( 90) covalent geometry : bond 0.00267 (30588) covalent geometry : angle 0.51343 (41562) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21374.40 seconds wall clock time: 369 minutes 23.29 seconds (22163.29 seconds total)