Starting phenix.real_space_refine on Thu Jun 26 15:03:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zrc_14910/06_2025/7zrc_14910.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrc_14910/06_2025/7zrc_14910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zrc_14910/06_2025/7zrc_14910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrc_14910/06_2025/7zrc_14910.map" model { file = "/net/cci-nas-00/data/ceres_data/7zrc_14910/06_2025/7zrc_14910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrc_14910/06_2025/7zrc_14910.cif" } resolution = 3.5 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= 0.002 sd= 0.027 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 140 5.16 5 C 19524 2.51 5 N 5064 2.21 5 O 5996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30724 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 8272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8272 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 54, 'TRANS': 1004} Chain breaks: 7 Chain: "C" Number of atoms: 8273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8273 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 53, 'TRANS': 1005} Chain breaks: 6 Chain: "A" Number of atoms: 8249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8249 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 53, 'TRANS': 1002} Chain breaks: 6 Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 900 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "F" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 900 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "J" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 900 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "K" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 18.37, per 1000 atoms: 0.60 Number of scatterers: 30724 At special positions: 0 Unit cell: (161.85, 161.02, 213.31, 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 140 16.00 O 5996 8.00 N 5064 7.00 C 19524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.02 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.02 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=2.03 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 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 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 J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 328 " " NAG A1304 " - " ASN A 600 " " NAG A1305 " - " ASN A 613 " " NAG A1306 " - " ASN A 654 " " NAG A1307 " - " ASN A 706 " " NAG A1308 " - " ASN A1071 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 340 " " NAG B1301 " - " ASN B 279 " " NAG B1302 " - " ASN B 328 " " NAG B1303 " - " ASN B 613 " " NAG B1304 " - " ASN B 654 " " NAG B1305 " - " ASN B 706 " " NAG B1306 " - " ASN B1071 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 340 " " NAG B1309 " - " ASN B 61 " " NAG C1301 " - " ASN C 61 " " 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 C1309 " - " ASN C 340 " " NAG D 1 " - " ASN B 798 " " NAG E 1 " - " ASN B 714 " " NAG I 1 " - " ASN B1095 " " NAG M 1 " - " ASN B1131 " " NAG N 1 " - " ASN C 714 " " NAG O 1 " - " ASN C 798 " " NAG P 1 " - " ASN C1095 " " NAG Q 1 " - " ASN C1131 " " NAG R 1 " - " ASN A 714 " " NAG S 1 " - " ASN A 798 " " NAG T 1 " - " ASN A1095 " " NAG U 1 " - " ASN A1131 " Time building additional restraints: 7.67 Conformation dependent library (CDL) restraints added in 3.9 seconds 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 71 sheets defined 21.5% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.86 Creating SS restraints... Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 338 Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.640A pdb=" N TRP B 350 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 380 through 386 removed outlier: 4.233A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.324A pdb=" N ARG B 405 " --> pdb=" O ASP 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 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.644A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.139A 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: 4.421A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.509A pdb=" N SER B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 338 Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 380 through 387 removed outlier: 4.164A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 387 " --> pdb=" O LEU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.331A pdb=" N ARG C 405 " --> pdb=" O ASP 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 756 through 780 Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.845A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.007A 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 removed outlier: 3.555A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1029 removed outlier: 3.536A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 4.017A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.674A pdb=" N TRP A 350 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 380 through 386 removed outlier: 4.210A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.476A pdb=" N ARG A 405 " --> pdb=" O ASP 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 613 through 617 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.798A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.743A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.260A 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 removed outlier: 3.549A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1029 removed outlier: 4.895A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 3.956A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.120A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.671A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.126A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.676A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 4.102A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.667A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.890A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 67 removed outlier: 3.544A pdb=" N ALA B 261 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.803A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.803A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N SER B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 143 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 308 through 316 removed outlier: 6.669A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 322 through 325 removed outlier: 5.734A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.568A pdb=" N TRP B 433 " --> pdb=" O ARG B 506 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.733A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.525A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 698 through 701 removed outlier: 6.264A pdb=" N VAL B 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LYS C 787 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN B 700 " --> pdb=" O LYS C 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.373A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.373A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.413A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 785 through 787 removed outlier: 5.645A pdb=" N ILE B 785 " --> pdb=" O ASN A 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.452A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AC2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.136A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 47 through 55 removed outlier: 6.371A pdb=" N LEU C 273 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA C 285 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS C 275 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.538A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.201A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.538A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR C 145 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 308 through 316 removed outlier: 6.630A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 321 through 325 removed outlier: 6.758A pdb=" N GLU C 321 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ASN C 539 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE C 323 " --> pdb=" O ASN C 539 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY C 563 " --> pdb=" O ASP C 571 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE C 562 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.602A pdb=" N TRP C 433 " --> pdb=" O ARG C 506 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.809A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AD2, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AD3, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.338A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 699 through 701 removed outlier: 3.628A pdb=" N LYS A 787 " --> pdb=" O ASN C 700 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 708 through 712 removed outlier: 4.442A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 715 through 725 removed outlier: 6.015A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 715 through 725 Processing sheet with id=AD8, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.524A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.341A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AE2, first strand: chain 'A' and resid 27 through 29 removed outlier: 3.521A pdb=" N ALA A 260 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.922A pdb=" N THR A 271 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP A 287 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.671A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 151 through 162 removed outlier: 5.626A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N SER A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 143 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 308 through 316 removed outlier: 6.636A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 321 through 325 removed outlier: 6.787A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 321 through 325 removed outlier: 6.787A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.541A pdb=" N TRP A 433 " --> pdb=" O ARG A 506 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.694A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AF3, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AF4, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.485A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.575A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 715 through 725 removed outlier: 7.058A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.459A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.938A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.938A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL H 107 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLY H 100 " --> pdb=" O PHE H 105 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE H 105 " --> pdb=" O GLY H 100 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.534A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AG5, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.591A pdb=" N TYR L 49 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AG7, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.925A pdb=" N THR F 112 " --> pdb=" O TYR F 94 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.925A pdb=" N THR F 112 " --> pdb=" O TYR F 94 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL F 107 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY F 100 " --> pdb=" O PHE F 105 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE F 105 " --> pdb=" O GLY F 100 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.523A pdb=" N VAL G 19 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AH2, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.579A pdb=" N TYR G 49 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AH4, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.867A pdb=" N THR J 112 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR J 33 " --> pdb=" O SER J 99 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.867A pdb=" N THR J 112 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY J 100 " --> pdb=" O PHE J 105 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N PHE J 105 " --> pdb=" O GLY J 100 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.521A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AH8, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.584A pdb=" N TYR K 49 " --> pdb=" O ASN K 53 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 1345 hydrogen bonds defined for protein. 3558 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: 16.81 Time building geometry restraints manager: 9.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9201 1.33 - 1.45: 5905 1.45 - 1.58: 16127 1.58 - 1.70: 0 1.70 - 1.82: 184 Bond restraints: 31417 Sorted by residual: bond pdb=" N ILE C 329 " pdb=" CA ILE C 329 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.82e+00 bond pdb=" N TYR C 263 " pdb=" CA TYR C 263 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.17e-02 7.31e+03 8.16e+00 bond pdb=" N GLN B1033 " pdb=" CA GLN B1033 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.15e+00 bond pdb=" N VAL A 607 " pdb=" CA VAL A 607 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.17e-02 7.31e+03 7.91e+00 bond pdb=" N VAL C 264 " pdb=" CA VAL C 264 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.22e-02 6.72e+03 7.87e+00 ... (remaining 31412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 41179 1.54 - 3.07: 1350 3.07 - 4.61: 179 4.61 - 6.14: 18 6.14 - 7.68: 5 Bond angle restraints: 42731 Sorted by residual: angle pdb=" N GLY C 854 " pdb=" CA GLY C 854 " pdb=" C GLY C 854 " ideal model delta sigma weight residual 114.92 108.42 6.50 1.30e+00 5.92e-01 2.50e+01 angle pdb=" C ASN K 30 " pdb=" CA ASN K 30 " pdb=" CB ASN K 30 " ideal model delta sigma weight residual 117.23 110.84 6.39 1.36e+00 5.41e-01 2.21e+01 angle pdb=" C ALA A 710 " pdb=" N ILE A 711 " pdb=" CA ILE A 711 " ideal model delta sigma weight residual 123.33 119.51 3.82 8.70e-01 1.32e+00 1.92e+01 angle pdb=" N ASN A 603 " pdb=" CA ASN A 603 " pdb=" C ASN A 603 " ideal model delta sigma weight residual 113.30 107.76 5.54 1.34e+00 5.57e-01 1.71e+01 angle pdb=" CA ASN A 61 " pdb=" CB ASN A 61 " pdb=" CG ASN A 61 " ideal model delta sigma weight residual 112.60 116.59 -3.99 1.00e+00 1.00e+00 1.59e+01 ... (remaining 42726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 18373 17.39 - 34.79: 805 34.79 - 52.18: 151 52.18 - 69.58: 30 69.58 - 86.97: 9 Dihedral angle restraints: 19368 sinusoidal: 8188 harmonic: 11180 Sorted by residual: dihedral pdb=" CB CYS C1079 " pdb=" SG CYS C1079 " pdb=" SG CYS C1123 " pdb=" CB CYS C1123 " ideal model delta sinusoidal sigma weight residual -86.00 -133.06 47.06 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CB CYS A1079 " pdb=" SG CYS A1079 " pdb=" SG CYS A1123 " pdb=" CB CYS A1123 " ideal model delta sinusoidal sigma weight residual -86.00 -132.11 46.11 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 298 " pdb=" CB CYS A 298 " ideal model delta sinusoidal sigma weight residual -86.00 -127.73 41.73 1 1.00e+01 1.00e-02 2.44e+01 ... (remaining 19365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 4900 0.122 - 0.244: 66 0.244 - 0.366: 2 0.366 - 0.488: 1 0.488 - 0.610: 1 Chirality restraints: 4970 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 328 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.31e+00 chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 4967 not shown) Planarity restraints: 5491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1309 " -0.229 2.00e-02 2.50e+03 1.92e-01 4.59e+02 pdb=" C7 NAG A1309 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A1309 " -0.162 2.00e-02 2.50e+03 pdb=" N2 NAG A1309 " 0.317 2.00e-02 2.50e+03 pdb=" O7 NAG A1309 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.223 2.00e-02 2.50e+03 1.84e-01 4.22e+02 pdb=" C7 NAG B1302 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.299 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1303 " -0.146 2.00e-02 2.50e+03 1.20e-01 1.80e+02 pdb=" C7 NAG A1303 " 0.041 2.00e-02 2.50e+03 pdb=" C8 NAG A1303 " -0.109 2.00e-02 2.50e+03 pdb=" N2 NAG A1303 " 0.191 2.00e-02 2.50e+03 pdb=" O7 NAG A1303 " 0.022 2.00e-02 2.50e+03 ... (remaining 5488 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 613 2.68 - 3.23: 28624 3.23 - 3.79: 47491 3.79 - 4.34: 66009 4.34 - 4.90: 110829 Nonbonded interactions: 253566 Sorted by model distance: nonbonded pdb=" O ALA A 876 " pdb=" OG1 THR A 880 " model vdw 2.125 3.040 nonbonded pdb=" O ALA C 876 " pdb=" OG1 THR C 880 " model vdw 2.138 3.040 nonbonded pdb=" OE2 GLU B 915 " pdb=" OG SER A1120 " model vdw 2.161 3.040 nonbonded pdb=" O GLY B 877 " pdb=" OG SER B 881 " model vdw 2.163 3.040 nonbonded pdb=" NH1 ARG A 902 " pdb=" O LEU A1046 " model vdw 2.167 3.120 ... (remaining 253561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 176 or resid 188 through 617 or resid 638 throu \ gh 1144 or resid 1301 through 1309)) selection = (chain 'B' and (resid 13 through 176 or resid 188 through 617 or resid 638 throu \ gh 1144 or resid 1301 through 1309)) selection = (chain 'C' and (resid 13 through 176 or resid 188 through 617 or resid 638 throu \ gh 1144 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' 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' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.920 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: 0.020 Extract box with map and model: 1.470 Check model and map are aligned: 0.250 Set scattering table: 0.300 Process input model: 77.220 Find NCS groups from input model: 1.970 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 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 : 0.006 0.125 31517 Z= 0.297 Angle : 0.661 21.914 42983 Z= 0.368 Chirality : 0.049 0.610 4970 Planarity : 0.006 0.192 5451 Dihedral : 10.102 86.971 12048 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 0.99 % Allowed : 4.91 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.03 (0.14), residues: 3797 helix: 1.31 (0.20), residues: 679 sheet: 0.02 (0.16), residues: 1074 loop : -0.44 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C1099 HIS 0.006 0.001 HIS C1085 PHE 0.020 0.002 PHE A1118 TYR 0.020 0.001 TYR B1064 ARG 0.005 0.000 ARG C1011 Details of bonding type rmsd link_NAG-ASN : bond 0.02042 ( 40) link_NAG-ASN : angle 3.28956 ( 120) link_BETA1-4 : bond 0.00196 ( 12) link_BETA1-4 : angle 1.20292 ( 36) hydrogen bonds : bond 0.13769 ( 1268) hydrogen bonds : angle 7.57905 ( 3558) SS BOND : bond 0.00335 ( 48) SS BOND : angle 1.17684 ( 96) covalent geometry : bond 0.00638 (31417) covalent geometry : angle 0.63665 (42731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 398 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.9181 (mt) cc_final: 0.8922 (mp) REVERT: B 177 MET cc_start: -0.2768 (ttm) cc_final: -0.4959 (mmt) REVERT: B 581 ILE cc_start: 0.8881 (mm) cc_final: 0.8659 (mp) REVERT: B 737 MET cc_start: 0.8286 (ttt) cc_final: 0.8037 (ttm) REVERT: B 981 LEU cc_start: 0.8926 (mt) cc_final: 0.8616 (mp) REVERT: C 302 SER cc_start: 0.8878 (t) cc_final: 0.8358 (p) REVERT: C 538 PHE cc_start: 0.8280 (p90) cc_final: 0.8022 (p90) REVERT: C 752 GLN cc_start: 0.8491 (mt0) cc_final: 0.8144 (mm-40) REVERT: C 864 ASP cc_start: 0.8365 (m-30) cc_final: 0.8158 (m-30) REVERT: C 1070 LYS cc_start: 0.8062 (mttt) cc_final: 0.7720 (mtpp) REVERT: A 164 ASN cc_start: 0.6444 (OUTLIER) cc_final: 0.5948 (p0) REVERT: A 773 LYS cc_start: 0.8032 (tttt) cc_final: 0.7813 (ttmm) REVERT: A 856 THR cc_start: 0.8834 (p) cc_final: 0.8629 (t) REVERT: A 954 GLN cc_start: 0.7537 (mm110) cc_final: 0.7252 (tp-100) REVERT: A 957 ASN cc_start: 0.8298 (m-40) cc_final: 0.8056 (m-40) REVERT: A 1007 GLN cc_start: 0.7839 (mt0) cc_final: 0.7621 (mp10) REVERT: H 48 MET cc_start: 0.1604 (mtp) cc_final: 0.1037 (ptm) outliers start: 33 outliers final: 15 residues processed: 428 average time/residue: 0.4143 time to fit residues: 283.0241 Evaluate side-chains 267 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 251 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 1078 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 6.9990 chunk 286 optimal weight: 0.7980 chunk 158 optimal weight: 0.4980 chunk 97 optimal weight: 0.6980 chunk 193 optimal weight: 1.9990 chunk 153 optimal weight: 40.0000 chunk 296 optimal weight: 1.9990 chunk 114 optimal weight: 0.0870 chunk 180 optimal weight: 0.2980 chunk 220 optimal weight: 20.0000 chunk 343 optimal weight: 10.0000 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN B 196 ASN B 752 GLN B 904 ASN B 954 GLN B 962 GLN B1007 GLN C 318 GLN C 537 ASN C 561 GLN C 759 GLN C 761 ASN C 946 GLN C 952 ASN C 962 GLN A 311 GLN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 577 GLN A 672 GLN A 910 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 GLN A 966 ASN L 101 GLN G 101 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.208658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.200336 restraints weight = 39313.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.199710 restraints weight = 93519.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.174022 restraints weight = 87378.790| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 31517 Z= 0.120 Angle : 0.542 12.476 42983 Z= 0.279 Chirality : 0.044 0.333 4970 Planarity : 0.004 0.048 5451 Dihedral : 6.226 59.561 5258 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.16 % Rotamer: Outliers : 1.38 % Allowed : 7.39 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.22 (0.14), residues: 3797 helix: 1.82 (0.20), residues: 669 sheet: 0.08 (0.16), residues: 1099 loop : -0.33 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 36 HIS 0.004 0.001 HIS A 49 PHE 0.018 0.001 PHE A 32 TYR 0.020 0.001 TYR B 262 ARG 0.003 0.000 ARG B 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 40) link_NAG-ASN : angle 2.53508 ( 120) link_BETA1-4 : bond 0.00492 ( 12) link_BETA1-4 : angle 0.99748 ( 36) hydrogen bonds : bond 0.03899 ( 1268) hydrogen bonds : angle 5.94141 ( 3558) SS BOND : bond 0.00469 ( 48) SS BOND : angle 1.35547 ( 96) covalent geometry : bond 0.00263 (31417) covalent geometry : angle 0.52167 (42731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 272 time to evaluate : 3.153 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: B 54 LEU cc_start: 0.9010 (mt) cc_final: 0.8779 (mp) REVERT: B 177 MET cc_start: -0.3072 (ttm) cc_final: -0.4842 (mmt) REVERT: B 581 ILE cc_start: 0.8605 (mm) cc_final: 0.8391 (mp) REVERT: B 658 GLU cc_start: 0.7308 (pm20) cc_final: 0.7100 (pm20) REVERT: B 954 GLN cc_start: 0.7539 (tt0) cc_final: 0.7212 (tp40) REVERT: C 177 MET cc_start: -0.3632 (mtp) cc_final: -0.4126 (mmt) REVERT: C 302 SER cc_start: 0.8374 (t) cc_final: 0.8084 (p) REVERT: C 736 THR cc_start: 0.8800 (m) cc_final: 0.8477 (p) REVERT: C 864 ASP cc_start: 0.7719 (m-30) cc_final: 0.7479 (m-30) REVERT: A 773 LYS cc_start: 0.7463 (tttt) cc_final: 0.6965 (ttpp) REVERT: A 856 THR cc_start: 0.8646 (p) cc_final: 0.8353 (t) REVERT: A 1007 GLN cc_start: 0.6318 (mt0) cc_final: 0.6076 (mp10) REVERT: H 48 MET cc_start: 0.2323 (mtp) cc_final: 0.1487 (ptm) outliers start: 46 outliers final: 25 residues processed: 307 average time/residue: 0.3884 time to fit residues: 199.4645 Evaluate side-chains 243 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 363 optimal weight: 0.4980 chunk 32 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 173 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 366 optimal weight: 50.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 952 ASN B1105 ASN B1139 GLN C 752 GLN C 932 GLN C 957 ASN C1007 GLN C1085 HIS A 49 HIS A 904 ASN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.205518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.197333 restraints weight = 39468.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.196672 restraints weight = 89939.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.176846 restraints weight = 95312.215| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 31517 Z= 0.249 Angle : 0.590 8.560 42983 Z= 0.304 Chirality : 0.047 0.324 4970 Planarity : 0.004 0.069 5451 Dihedral : 5.930 58.388 5245 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 2.18 % Allowed : 8.50 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 3797 helix: 1.38 (0.20), residues: 673 sheet: 0.04 (0.15), residues: 1110 loop : -0.43 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 36 HIS 0.006 0.001 HIS B 207 PHE 0.023 0.002 PHE B 487 TYR 0.019 0.001 TYR B1064 ARG 0.004 0.000 ARG C1011 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 40) link_NAG-ASN : angle 2.23263 ( 120) link_BETA1-4 : bond 0.00274 ( 12) link_BETA1-4 : angle 1.15150 ( 36) hydrogen bonds : bond 0.04506 ( 1268) hydrogen bonds : angle 5.91847 ( 3558) SS BOND : bond 0.00469 ( 48) SS BOND : angle 1.45586 ( 96) covalent geometry : bond 0.00599 (31417) covalent geometry : angle 0.57483 (42731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 227 time to evaluate : 3.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.2644 (ttm) cc_final: -0.4681 (mmt) REVERT: B 899 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7721 (mmm) REVERT: B 947 ASP cc_start: 0.7616 (m-30) cc_final: 0.7379 (m-30) REVERT: C 302 SER cc_start: 0.8620 (t) cc_final: 0.8287 (p) REVERT: C 864 ASP cc_start: 0.7946 (m-30) cc_final: 0.7724 (m-30) REVERT: C 985 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6364 (tm-30) REVERT: C 1042 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.6965 (mtpp) REVERT: A 299 THR cc_start: 0.8752 (m) cc_final: 0.8521 (p) REVERT: A 856 THR cc_start: 0.8608 (p) cc_final: 0.8321 (t) REVERT: H 48 MET cc_start: 0.1826 (mtp) cc_final: 0.1130 (ptm) outliers start: 73 outliers final: 49 residues processed: 287 average time/residue: 0.3783 time to fit residues: 184.7319 Evaluate side-chains 263 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 211 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 377 optimal weight: 20.0000 chunk 279 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 313 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 237 optimal weight: 2.9990 chunk 138 optimal weight: 40.0000 chunk 291 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 333 optimal weight: 50.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 610 GLN C 385 ASN C 759 GLN C 957 ASN A 311 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 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 = 0.4319 r_free = 0.4319 target = 0.206913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.198458 restraints weight = 39441.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.174035 restraints weight = 96651.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.163517 restraints weight = 83342.108| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31517 Z= 0.134 Angle : 0.522 8.370 42983 Z= 0.269 Chirality : 0.044 0.306 4970 Planarity : 0.004 0.067 5451 Dihedral : 5.358 58.481 5245 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.66 % Favored : 97.31 % Rotamer: Outliers : 1.94 % Allowed : 9.58 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.17 (0.14), residues: 3797 helix: 1.67 (0.20), residues: 672 sheet: 0.09 (0.15), residues: 1098 loop : -0.34 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.003 0.001 HIS A 207 PHE 0.019 0.001 PHE B 487 TYR 0.017 0.001 TYR B1064 ARG 0.004 0.000 ARG B 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 40) link_NAG-ASN : angle 2.03262 ( 120) link_BETA1-4 : bond 0.00302 ( 12) link_BETA1-4 : angle 1.03198 ( 36) hydrogen bonds : bond 0.03784 ( 1268) hydrogen bonds : angle 5.61039 ( 3558) SS BOND : bond 0.00375 ( 48) SS BOND : angle 1.09904 ( 96) covalent geometry : bond 0.00309 (31417) covalent geometry : angle 0.50914 (42731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 220 time to evaluate : 3.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.2975 (ttm) cc_final: -0.4748 (mmt) REVERT: B 947 ASP cc_start: 0.7701 (m-30) cc_final: 0.7446 (m-30) REVERT: C 177 MET cc_start: -0.3350 (mmm) cc_final: -0.4035 (mmt) REVERT: C 302 SER cc_start: 0.8668 (t) cc_final: 0.8324 (p) REVERT: C 864 ASP cc_start: 0.7826 (m-30) cc_final: 0.7603 (m-30) REVERT: C 1042 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7020 (mtpp) REVERT: A 299 THR cc_start: 0.8736 (m) cc_final: 0.8456 (p) REVERT: A 856 THR cc_start: 0.8590 (p) cc_final: 0.8344 (t) REVERT: A 1042 LYS cc_start: 0.7208 (tttt) cc_final: 0.6924 (mptt) REVERT: H 48 MET cc_start: 0.2253 (mtp) cc_final: 0.1400 (ptm) outliers start: 65 outliers final: 43 residues processed: 273 average time/residue: 0.3890 time to fit residues: 180.7805 Evaluate side-chains 254 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 155 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 105 optimal weight: 50.0000 chunk 237 optimal weight: 4.9990 chunk 345 optimal weight: 10.0000 chunk 205 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 42 optimal weight: 50.0000 chunk 279 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 40.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 946 GLN A 268 GLN A 672 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.204128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.194966 restraints weight = 39141.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.170752 restraints weight = 101884.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.162016 restraints weight = 88487.579| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 31517 Z= 0.298 Angle : 0.610 8.611 42983 Z= 0.315 Chirality : 0.048 0.320 4970 Planarity : 0.004 0.073 5451 Dihedral : 5.501 57.337 5245 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 2.60 % Allowed : 9.52 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 (0.13), residues: 3797 helix: 1.14 (0.20), residues: 674 sheet: 0.00 (0.15), residues: 1087 loop : -0.44 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 104 HIS 0.005 0.001 HIS A1045 PHE 0.023 0.002 PHE C 756 TYR 0.019 0.001 TYR B1064 ARG 0.005 0.000 ARG C1011 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 40) link_NAG-ASN : angle 2.27377 ( 120) link_BETA1-4 : bond 0.00308 ( 12) link_BETA1-4 : angle 1.20810 ( 36) hydrogen bonds : bond 0.04650 ( 1268) hydrogen bonds : angle 5.84193 ( 3558) SS BOND : bond 0.00603 ( 48) SS BOND : angle 1.25919 ( 96) covalent geometry : bond 0.00718 (31417) covalent geometry : angle 0.59535 (42731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 207 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.2946 (ttm) cc_final: -0.4459 (mmt) REVERT: B 947 ASP cc_start: 0.7731 (m-30) cc_final: 0.7452 (m-30) REVERT: B 954 GLN cc_start: 0.7654 (tt0) cc_final: 0.7232 (tp40) REVERT: C 177 MET cc_start: -0.3152 (mmm) cc_final: -0.3917 (mmt) REVERT: C 302 SER cc_start: 0.8478 (t) cc_final: 0.8151 (p) REVERT: C 985 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6284 (tm-30) REVERT: C 1042 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.6993 (mtpp) REVERT: A 299 THR cc_start: 0.8801 (m) cc_final: 0.8498 (p) REVERT: A 537 ASN cc_start: 0.7980 (t0) cc_final: 0.7749 (t0) REVERT: A 856 THR cc_start: 0.8634 (p) cc_final: 0.8342 (t) REVERT: H 48 MET cc_start: 0.2116 (mtp) cc_final: 0.1317 (ptm) REVERT: K 4 MET cc_start: 0.4149 (tmm) cc_final: 0.3499 (tpt) outliers start: 87 outliers final: 65 residues processed: 280 average time/residue: 0.3756 time to fit residues: 179.7447 Evaluate side-chains 266 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 199 time to evaluate : 3.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 317 optimal weight: 50.0000 chunk 67 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 201 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 305 optimal weight: 0.6980 chunk 271 optimal weight: 0.9980 chunk 250 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 946 GLN A 759 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.206430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.198347 restraints weight = 39355.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.197584 restraints weight = 88947.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.178498 restraints weight = 88158.006| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31517 Z= 0.125 Angle : 0.520 18.308 42983 Z= 0.265 Chirality : 0.044 0.295 4970 Planarity : 0.004 0.071 5451 Dihedral : 4.986 55.264 5245 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 1.92 % Allowed : 10.11 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.17 (0.14), residues: 3797 helix: 1.70 (0.20), residues: 661 sheet: 0.12 (0.15), residues: 1073 loop : -0.36 (0.14), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 104 HIS 0.002 0.001 HIS C 49 PHE 0.018 0.001 PHE B 487 TYR 0.022 0.001 TYR A1135 ARG 0.002 0.000 ARG B 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 40) link_NAG-ASN : angle 2.85299 ( 120) link_BETA1-4 : bond 0.00371 ( 12) link_BETA1-4 : angle 1.03633 ( 36) hydrogen bonds : bond 0.03654 ( 1268) hydrogen bonds : angle 5.46277 ( 3558) SS BOND : bond 0.00321 ( 48) SS BOND : angle 0.90352 ( 96) covalent geometry : bond 0.00282 (31417) covalent geometry : angle 0.49657 (42731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 212 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.3178 (ttm) cc_final: -0.4036 (mmt) REVERT: B 947 ASP cc_start: 0.7635 (m-30) cc_final: 0.7421 (m-30) REVERT: B 954 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7129 (tp40) REVERT: C 302 SER cc_start: 0.8739 (t) cc_final: 0.8425 (p) REVERT: C 1042 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7032 (mtpp) REVERT: A 299 THR cc_start: 0.8745 (m) cc_final: 0.8462 (p) REVERT: A 856 THR cc_start: 0.8582 (p) cc_final: 0.8266 (t) REVERT: H 48 MET cc_start: 0.1594 (mtp) cc_final: 0.0968 (ptm) REVERT: K 4 MET cc_start: 0.3770 (tmm) cc_final: 0.3251 (tpt) outliers start: 64 outliers final: 51 residues processed: 269 average time/residue: 0.3919 time to fit residues: 180.1835 Evaluate side-chains 255 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 202 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 117 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 333 optimal weight: 50.0000 chunk 65 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 311 GLN A 672 GLN A 759 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** K 90 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 = 0.4300 r_free = 0.4300 target = 0.204942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.196289 restraints weight = 39209.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.195647 restraints weight = 97663.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.177234 restraints weight = 99359.332| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 31517 Z= 0.214 Angle : 0.562 17.142 42983 Z= 0.287 Chirality : 0.046 0.302 4970 Planarity : 0.004 0.072 5451 Dihedral : 5.036 52.433 5245 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.71 % Rotamer: Outliers : 2.15 % Allowed : 10.14 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 3797 helix: 1.47 (0.20), residues: 670 sheet: 0.09 (0.15), residues: 1091 loop : -0.37 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 104 HIS 0.003 0.001 HIS A1045 PHE 0.019 0.002 PHE B1118 TYR 0.024 0.001 TYR C1135 ARG 0.004 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 40) link_NAG-ASN : angle 2.84354 ( 120) link_BETA1-4 : bond 0.00214 ( 12) link_BETA1-4 : angle 1.08495 ( 36) hydrogen bonds : bond 0.04149 ( 1268) hydrogen bonds : angle 5.55109 ( 3558) SS BOND : bond 0.00416 ( 48) SS BOND : angle 1.39339 ( 96) covalent geometry : bond 0.00511 (31417) covalent geometry : angle 0.53776 (42731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 197 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.3163 (ttm) cc_final: -0.4346 (mmt) REVERT: B 947 ASP cc_start: 0.7689 (m-30) cc_final: 0.7471 (m-30) REVERT: B 954 GLN cc_start: 0.7591 (tt0) cc_final: 0.7212 (tp40) REVERT: C 302 SER cc_start: 0.8690 (t) cc_final: 0.8339 (p) REVERT: C 1042 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7025 (mtpp) REVERT: A 856 THR cc_start: 0.8576 (p) cc_final: 0.8240 (t) REVERT: H 48 MET cc_start: 0.1523 (mtp) cc_final: 0.0874 (ptm) REVERT: K 4 MET cc_start: 0.3671 (tmm) cc_final: 0.2981 (tpt) outliers start: 72 outliers final: 63 residues processed: 258 average time/residue: 0.3893 time to fit residues: 173.1022 Evaluate side-chains 255 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 191 time to evaluate : 3.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1094 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 77 optimal weight: 0.4980 chunk 335 optimal weight: 9.9990 chunk 264 optimal weight: 0.7980 chunk 365 optimal weight: 30.0000 chunk 20 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 330 optimal weight: 40.0000 chunk 281 optimal weight: 0.6980 chunk 204 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 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 268 GLN A 311 GLN A 759 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.206445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.198297 restraints weight = 39337.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.197652 restraints weight = 87858.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.175284 restraints weight = 89756.560| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31517 Z= 0.124 Angle : 0.512 15.971 42983 Z= 0.261 Chirality : 0.044 0.289 4970 Planarity : 0.004 0.064 5451 Dihedral : 4.718 46.385 5245 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 1.77 % Allowed : 10.47 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.27 (0.14), residues: 3797 helix: 1.84 (0.20), residues: 663 sheet: 0.19 (0.16), residues: 1075 loop : -0.32 (0.14), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 104 HIS 0.002 0.000 HIS A 207 PHE 0.014 0.001 PHE C 92 TYR 0.019 0.001 TYR A1135 ARG 0.003 0.000 ARG B 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 40) link_NAG-ASN : angle 2.62383 ( 120) link_BETA1-4 : bond 0.00308 ( 12) link_BETA1-4 : angle 1.02412 ( 36) hydrogen bonds : bond 0.03592 ( 1268) hydrogen bonds : angle 5.33532 ( 3558) SS BOND : bond 0.00321 ( 48) SS BOND : angle 1.11411 ( 96) covalent geometry : bond 0.00282 (31417) covalent geometry : angle 0.49045 (42731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 207 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.3352 (ttm) cc_final: -0.4342 (mmt) REVERT: B 954 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7158 (tp40) REVERT: C 302 SER cc_start: 0.8792 (t) cc_final: 0.8449 (p) REVERT: C 1042 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7098 (mtpp) REVERT: A 856 THR cc_start: 0.8577 (p) cc_final: 0.8281 (t) REVERT: A 1007 GLN cc_start: 0.6458 (OUTLIER) cc_final: 0.6086 (pt0) REVERT: H 48 MET cc_start: 0.1785 (mtp) cc_final: 0.1050 (ptm) REVERT: K 4 MET cc_start: 0.3677 (tmm) cc_final: 0.3163 (tpt) outliers start: 59 outliers final: 53 residues processed: 257 average time/residue: 0.4056 time to fit residues: 177.2143 Evaluate side-chains 249 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 3.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 7 optimal weight: 0.7980 chunk 247 optimal weight: 8.9990 chunk 287 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 365 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 263 optimal weight: 0.9980 chunk 358 optimal weight: 0.0370 chunk 110 optimal weight: 0.0040 chunk 72 optimal weight: 1.9990 overall best weight: 0.5270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 759 GLN A 268 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN A 954 GLN ** K 90 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 = 0.4324 r_free = 0.4324 target = 0.207310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.199479 restraints weight = 39276.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.198738 restraints weight = 86452.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.173322 restraints weight = 85313.996| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31517 Z= 0.105 Angle : 0.504 15.277 42983 Z= 0.256 Chirality : 0.043 0.284 4970 Planarity : 0.003 0.059 5451 Dihedral : 4.460 45.011 5245 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 1.68 % Allowed : 10.92 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.40 (0.14), residues: 3797 helix: 2.03 (0.20), residues: 666 sheet: 0.26 (0.16), residues: 1070 loop : -0.27 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 104 HIS 0.002 0.001 HIS A 207 PHE 0.014 0.001 PHE C 92 TYR 0.019 0.001 TYR K 49 ARG 0.011 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 40) link_NAG-ASN : angle 2.50588 ( 120) link_BETA1-4 : bond 0.00339 ( 12) link_BETA1-4 : angle 1.01139 ( 36) hydrogen bonds : bond 0.03440 ( 1268) hydrogen bonds : angle 5.20036 ( 3558) SS BOND : bond 0.00275 ( 48) SS BOND : angle 0.98048 ( 96) covalent geometry : bond 0.00234 (31417) covalent geometry : angle 0.48450 (42731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 209 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.3493 (ttm) cc_final: -0.4274 (mmt) REVERT: B 954 GLN cc_start: 0.7503 (tt0) cc_final: 0.7165 (tp40) REVERT: C 177 MET cc_start: -0.3865 (mmt) cc_final: -0.4823 (mtt) REVERT: C 302 SER cc_start: 0.8762 (t) cc_final: 0.8421 (p) REVERT: C 571 ASP cc_start: 0.7551 (t0) cc_final: 0.7348 (t0) REVERT: C 1042 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7171 (mtpp) REVERT: A 856 THR cc_start: 0.8569 (p) cc_final: 0.8253 (t) REVERT: A 1007 GLN cc_start: 0.6868 (OUTLIER) cc_final: 0.6084 (pt0) REVERT: H 48 MET cc_start: 0.2049 (mtp) cc_final: 0.1202 (ptm) REVERT: K 4 MET cc_start: 0.3902 (tmm) cc_final: 0.3408 (tpt) outliers start: 56 outliers final: 50 residues processed: 256 average time/residue: 0.4441 time to fit residues: 195.5113 Evaluate side-chains 249 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 361 optimal weight: 50.0000 chunk 360 optimal weight: 6.9990 chunk 286 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 chunk 222 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 357 ASN C 759 GLN A 268 GLN A 311 GLN A 759 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 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 = 0.4301 r_free = 0.4301 target = 0.204957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.197027 restraints weight = 39119.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.196285 restraints weight = 87031.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.172220 restraints weight = 83245.707| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 : 0.005 0.083 31517 Z= 0.212 Angle : 0.562 14.327 42983 Z= 0.287 Chirality : 0.046 0.296 4970 Planarity : 0.004 0.061 5451 Dihedral : 4.741 47.417 5245 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 1.80 % Allowed : 10.86 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.22 (0.14), residues: 3797 helix: 1.64 (0.20), residues: 666 sheet: 0.21 (0.16), residues: 1078 loop : -0.33 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 104 HIS 0.005 0.001 HIS A1045 PHE 0.020 0.002 PHE A 344 TYR 0.017 0.001 TYR B1064 ARG 0.005 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 40) link_NAG-ASN : angle 2.57419 ( 120) link_BETA1-4 : bond 0.00249 ( 12) link_BETA1-4 : angle 1.08004 ( 36) hydrogen bonds : bond 0.04130 ( 1268) hydrogen bonds : angle 5.44032 ( 3558) SS BOND : bond 0.00405 ( 48) SS BOND : angle 1.22024 ( 96) covalent geometry : bond 0.00507 (31417) covalent geometry : angle 0.54338 (42731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 202 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.3315 (ttm) cc_final: -0.4255 (mmt) REVERT: B 954 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7285 (tp40) REVERT: C 177 MET cc_start: -0.3418 (mmt) cc_final: -0.4586 (mtt) REVERT: C 302 SER cc_start: 0.8745 (t) cc_final: 0.8407 (p) REVERT: C 1042 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7017 (mtpp) REVERT: A 856 THR cc_start: 0.8622 (p) cc_final: 0.8291 (t) REVERT: A 909 THR cc_start: 0.8370 (m) cc_final: 0.8007 (p) REVERT: A 1007 GLN cc_start: 0.6000 (OUTLIER) cc_final: 0.5403 (mp10) REVERT: H 48 MET cc_start: 0.1875 (mtp) cc_final: 0.1071 (ptm) REVERT: K 4 MET cc_start: 0.3854 (tmm) cc_final: 0.3305 (tpt) outliers start: 60 outliers final: 52 residues processed: 254 average time/residue: 0.3657 time to fit residues: 159.6504 Evaluate side-chains 256 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1094 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 87 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 chunk 247 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 0 optimal weight: 50.0000 chunk 170 optimal weight: 0.5980 chunk 357 optimal weight: 8.9990 chunk 196 optimal weight: 0.9980 chunk 337 optimal weight: 40.0000 chunk 173 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 357 ASN A 311 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.205925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.198143 restraints weight = 39137.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.197540 restraints weight = 87414.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.174538 restraints weight = 93177.789| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31517 Z= 0.149 Angle : 0.530 13.909 42983 Z= 0.270 Chirality : 0.044 0.289 4970 Planarity : 0.004 0.058 5451 Dihedral : 4.608 46.714 5245 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.97 % Rotamer: Outliers : 1.68 % Allowed : 11.04 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.31 (0.14), residues: 3797 helix: 1.78 (0.20), residues: 668 sheet: 0.24 (0.16), residues: 1072 loop : -0.29 (0.14), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 104 HIS 0.003 0.001 HIS A 207 PHE 0.019 0.001 PHE A 344 TYR 0.027 0.001 TYR A1135 ARG 0.006 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 40) link_NAG-ASN : angle 2.45546 ( 120) link_BETA1-4 : bond 0.00306 ( 12) link_BETA1-4 : angle 1.04157 ( 36) hydrogen bonds : bond 0.03737 ( 1268) hydrogen bonds : angle 5.32339 ( 3558) SS BOND : bond 0.00337 ( 48) SS BOND : angle 1.10376 ( 96) covalent geometry : bond 0.00349 (31417) covalent geometry : angle 0.51204 (42731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9546.35 seconds wall clock time: 167 minutes 47.40 seconds (10067.40 seconds total)