Starting phenix.real_space_refine on Mon Sep 14 08:59:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xo2_67067/09_2026/9xo2_67067.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xo2_67067/09_2026/9xo2_67067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xo2_67067/09_2026/9xo2_67067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xo2_67067/09_2026/9xo2_67067.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xo2_67067/09_2026/9xo2_67067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xo2_67067/09_2026/9xo2_67067.map" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.082 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 18231 2.51 5 N 4633 2.21 5 O 5704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28708 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1104, 8489 Classifications: {'peptide': 1104} Link IDs: {'PTRANS': 40, 'TRANS': 1063} Chain breaks: 12 Chain: "F" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 881 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "G" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 743 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 8, 'TRANS': 93} Chain: "B" Number of atoms: 8823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1149, 8823 Classifications: {'peptide': 1149} Link IDs: {'PTRANS': 42, 'TRANS': 1106} Chain breaks: 8 Chain: "C" Number of atoms: 8823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1149, 8823 Classifications: {'peptide': 1149} Link IDs: {'PTRANS': 42, 'TRANS': 1106} Chain breaks: 8 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 162 Unusual residues: {'NAG': 9, 'PAM': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 222 Unusual residues: {'NAG': 12, 'PAM': 3} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 186 Unusual residues: {'NAG': 12, 'PAM': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 6.65, per 1000 atoms: 0.23 Number of scatterers: 28708 At special positions: 0 Unit cell: (169.26, 194.37, 166.47, 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 5704 8.00 N 4633 7.00 C 18231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.02 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.03 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.03 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 67 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 473 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 589 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 599 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 830 " distance=2.03 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 819 " distance=2.03 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 931 " distance=2.03 Simple disulfide: pdb=" SG CYS B1122 " - pdb=" SG CYS B1133 " distance=2.03 Simple disulfide: pdb=" SG CYS B1173 " - pdb=" SG CYS B1226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 196 " - pdb=" SG CYS C 202 " distance=2.02 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 373 " distance=2.03 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 543 " - pdb=" SG CYS C 589 " distance=2.03 Simple disulfide: pdb=" SG CYS C 572 " - pdb=" SG CYS C 599 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 700 " distance=2.04 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 830 " distance=2.03 Simple disulfide: pdb=" SG CYS C 813 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS C 920 " - pdb=" SG CYS C 931 " distance=2.03 Simple disulfide: pdb=" SG CYS C1122 " - pdb=" SG CYS C1133 " distance=2.03 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1226 " 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 ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " " BMA M 3 " - " MAN M 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1401 " - " ASN A 324 " " NAG A1402 " - " ASN A 344 " " NAG A1403 " - " ASN A 726 " " NAG A1404 " - " ASN A 781 " " NAG A1405 " - " ASN A 514 " " NAG A1406 " - " ASN A 556 " " NAG A1407 " - " ASN A 743 " " NAG A1408 " - " ASN A 787 " " NAG A1409 " - " ASN A1009 " " NAG B1402 " - " ASN B 324 " " NAG B1403 " - " ASN B 216 " " NAG B1404 " - " ASN B 514 " " NAG B1405 " - " ASN B 726 " " NAG B1406 " - " ASN B 781 " " NAG B1407 " - " ASN B 743 " " NAG B1408 " - " ASN B 787 " " NAG B1409 " - " ASN B 873 " " NAG B1410 " - " ASN B1009 " " NAG B1411 " - " ASN B1232 " " NAG B1412 " - " ASN B 344 " " NAG B1413 " - " ASN B 351 " " NAG C1401 " - " ASN C 324 " " NAG C1402 " - " ASN C 216 " " NAG C1403 " - " ASN C 514 " " NAG C1404 " - " ASN C 726 " " NAG C1405 " - " ASN C 781 " " NAG C1406 " - " ASN C 743 " " NAG C1407 " - " ASN C 787 " " NAG C1408 " - " ASN C 873 " " NAG C1409 " - " ASN C1009 " " NAG C1410 " - " ASN C1232 " " NAG C1411 " - " ASN C 344 " " NAG C1412 " - " ASN C 351 " " NAG D 1 " - " ASN A 216 " " NAG E 1 " - " ASN A 688 " " NAG H 1 " - " ASN A 873 " " NAG I 1 " - " ASN A 264 " " NAG J 1 " - " ASN B 264 " " NAG K 1 " - " ASN B 688 " " NAG L 1 " - " ASN B 425 " " NAG M 1 " - " ASN C 264 " " NAG N 1 " - " ASN C 688 " " NAG O 1 " - " ASN C 425 " Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.4 seconds 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6676 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 58 sheets defined 21.4% alpha, 38.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 233 through 241 removed outlier: 3.722A pdb=" N ALA A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 removed outlier: 3.567A pdb=" N ILE A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 807 through 814 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 828 through 852 Processing helix chain 'A' and resid 855 through 860 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 917 through 922 removed outlier: 3.708A pdb=" N SER A 921 " --> pdb=" O LYS A 918 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A 922 " --> pdb=" O ARG A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 935 Processing helix chain 'A' and resid 946 through 960 Processing helix chain 'A' and resid 961 through 963 No H-bonds generated for 'chain 'A' and resid 961 through 963' Processing helix chain 'A' and resid 973 through 986 removed outlier: 3.900A pdb=" N ALA A 977 " --> pdb=" O PRO A 973 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1014 Processing helix chain 'A' and resid 1030 through 1045 removed outlier: 3.570A pdb=" N GLN A1045 " --> pdb=" O VAL A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1055 Processing helix chain 'A' and resid 1056 through 1058 No H-bonds generated for 'chain 'A' and resid 1056 through 1058' Processing helix chain 'A' and resid 1066 through 1074 Processing helix chain 'A' and resid 1075 through 1123 Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'F' and resid 106 through 110 removed outlier: 3.842A pdb=" N ALA F 110 " --> pdb=" O THR F 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 99 through 103 removed outlier: 3.589A pdb=" N ASP G 102 " --> pdb=" O GLN G 99 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU G 103 " --> pdb=" O ALA G 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 99 through 103' Processing helix chain 'B' and resid 33 through 38 removed outlier: 3.575A pdb=" N LYS B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.593A pdb=" N GLY B 224 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE B 225 " --> pdb=" O GLU B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 225' Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.637A pdb=" N VAL B 328 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.957A pdb=" N ALA B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 475 Processing helix chain 'B' and resid 807 through 813 Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.560A pdb=" N THR B 824 " --> pdb=" O LYS B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 852 removed outlier: 3.719A pdb=" N ILE B 833 " --> pdb=" O ALA B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 861 removed outlier: 3.673A pdb=" N LEU B 861 " --> pdb=" O GLU B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 878 removed outlier: 3.709A pdb=" N LEU B 878 " --> pdb=" O THR B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 903 Processing helix chain 'B' and resid 917 through 922 removed outlier: 3.693A pdb=" N SER B 921 " --> pdb=" O LYS B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 935 Processing helix chain 'B' and resid 946 through 960 Processing helix chain 'B' and resid 961 through 963 No H-bonds generated for 'chain 'B' and resid 961 through 963' Processing helix chain 'B' and resid 973 through 986 removed outlier: 3.760A pdb=" N ALA B 977 " --> pdb=" O PRO B 973 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 984 " --> pdb=" O ALA B 980 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU B 985 " --> pdb=" O ARG B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1016 Processing helix chain 'B' and resid 1030 through 1044 Processing helix chain 'B' and resid 1046 through 1054 Processing helix chain 'B' and resid 1055 through 1058 Processing helix chain 'B' and resid 1066 through 1074 Processing helix chain 'B' and resid 1075 through 1123 removed outlier: 3.692A pdb=" N ASP B1080 " --> pdb=" O ILE B1076 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG B1085 " --> pdb=" O VAL B1081 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B1086 " --> pdb=" O GLN B1082 " (cutoff:3.500A) Processing helix chain 'B' and resid 1216 through 1218 No H-bonds generated for 'chain 'B' and resid 1216 through 1218' Processing helix chain 'B' and resid 1237 through 1242 removed outlier: 3.606A pdb=" N VAL B1241 " --> pdb=" O GLN B1237 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.561A pdb=" N GLY C 224 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE C 225 " --> pdb=" O GLU C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 225' Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.706A pdb=" N TYR C 237 " --> pdb=" O CYS C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 removed outlier: 3.680A pdb=" N VAL C 328 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 removed outlier: 3.530A pdb=" N LEU C 357 " --> pdb=" O ASP C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 807 through 813 Processing helix chain 'C' and resid 816 through 825 removed outlier: 4.160A pdb=" N GLN C 825 " --> pdb=" O GLN C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 852 removed outlier: 3.834A pdb=" N ILE C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 860 removed outlier: 3.667A pdb=" N GLN C 860 " --> pdb=" O GLU C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 Processing helix chain 'C' and resid 917 through 921 removed outlier: 3.509A pdb=" N SER C 921 " --> pdb=" O LYS C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 935 Processing helix chain 'C' and resid 946 through 960 Processing helix chain 'C' and resid 973 through 986 removed outlier: 3.778A pdb=" N ALA C 977 " --> pdb=" O PRO C 973 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 984 " --> pdb=" O ALA C 980 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU C 985 " --> pdb=" O ARG C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1016 removed outlier: 3.560A pdb=" N GLU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1044 Processing helix chain 'C' and resid 1046 through 1054 Processing helix chain 'C' and resid 1055 through 1058 removed outlier: 3.611A pdb=" N HIS C1058 " --> pdb=" O GLN C1055 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1055 through 1058' Processing helix chain 'C' and resid 1066 through 1074 Processing helix chain 'C' and resid 1075 through 1123 removed outlier: 3.634A pdb=" N ASP C1080 " --> pdb=" O ILE C1076 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C1081 " --> pdb=" O LEU C1077 " (cutoff:3.500A) Processing helix chain 'C' and resid 1216 through 1218 No H-bonds generated for 'chain 'C' and resid 1216 through 1218' Processing helix chain 'C' and resid 1234 through 1236 No H-bonds generated for 'chain 'C' and resid 1234 through 1236' Processing helix chain 'C' and resid 1237 through 1242 removed outlier: 3.593A pdb=" N VAL C1241 " --> pdb=" O GLN C1237 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.676A pdb=" N ALA A 74 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 91 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 125 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLN A 127 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASN A 147 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.676A pdb=" N ALA A 74 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 91 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 286 removed outlier: 7.533A pdb=" N VAL A 273 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A 453 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER A 275 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE A 451 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLN A 277 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA A 449 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU A 279 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL A 447 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 440 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASP A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 414 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 270 through 286 removed outlier: 7.533A pdb=" N VAL A 273 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A 453 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER A 275 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE A 451 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLN A 277 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA A 449 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU A 279 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL A 447 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ASP A 448 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TYR A 463 " --> pdb=" O ASP A 448 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU A 450 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A 461 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLU A 452 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 295 through 298 removed outlier: 6.982A pdb=" N HIS A 338 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL A 422 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 336 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 424 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER A 334 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN A 344 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 348 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TYR A 371 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL A 390 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N CYS A 373 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 483 through 488 removed outlier: 3.729A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 499 through 502 removed outlier: 3.538A pdb=" N GLY A 659 " --> pdb=" O TYR A 652 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL A 694 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 526 through 536 removed outlier: 5.491A pdb=" N ASN A 528 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER A 520 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 532 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N SER A 518 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR A 534 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR A 516 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE A 536 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN A 514 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 587 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY A 625 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE A 585 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 526 through 536 removed outlier: 5.491A pdb=" N ASN A 528 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER A 520 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 532 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N SER A 518 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR A 534 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR A 516 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE A 536 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN A 514 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS A 614 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY A 605 " --> pdb=" O LYS A 614 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 616 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 749 through 750 Processing sheet with id=AB4, first strand: chain 'A' and resid 780 through 798 removed outlier: 7.016A pdb=" N ASN A 781 " --> pdb=" O ILE A1167 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE A1167 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER A 783 " --> pdb=" O ASP A1165 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP A1165 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE A1163 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN A 787 " --> pdb=" O GLY A1161 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A1141 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A1158 " --> pdb=" O HIS A1139 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N HIS A1139 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 780 through 798 removed outlier: 7.016A pdb=" N ASN A 781 " --> pdb=" O ILE A1167 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE A1167 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER A 783 " --> pdb=" O ASP A1165 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP A1165 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE A1163 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN A 787 " --> pdb=" O GLY A1161 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A1167 " --> pdb=" O THR A1191 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A1191 " --> pdb=" O ILE A1167 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A1189 " --> pdb=" O ILE A1169 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB7, first strand: chain 'A' and resid 1171 through 1174 Processing sheet with id=AB8, first strand: chain 'F' and resid 23 through 26 removed outlier: 3.610A pdb=" N LEU F 100 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR F 97 " --> pdb=" O ASP F 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 77 through 79 removed outlier: 6.595A pdb=" N TRP F 55 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY F 69 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE F 53 " --> pdb=" O GLY F 69 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL F 56 " --> pdb=" O TYR F 114 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 22 through 24 removed outlier: 3.812A pdb=" N ALA G 41 " --> pdb=" O ILE G 23 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AC3, first strand: chain 'G' and resid 65 through 68 removed outlier: 5.861A pdb=" N LEU G 66 " --> pdb=" O GLN G 57 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN G 57 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET G 68 " --> pdb=" O TRP G 55 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER G 54 " --> pdb=" O LYS G 109 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL G 105 " --> pdb=" O GLN G 58 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 85 through 87 removed outlier: 3.541A pdb=" N GLY G 85 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 23 through 25 Processing sheet with id=AC6, first strand: chain 'B' and resid 45 through 49 Processing sheet with id=AC7, first strand: chain 'B' and resid 69 through 70 removed outlier: 3.678A pdb=" N GLY B 69 " --> pdb=" O CYS B 196 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS B 196 " --> pdb=" O GLY B 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 74 through 75 removed outlier: 3.521A pdb=" N ARG B 191 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 180 through 184 removed outlier: 3.732A pdb=" N GLY B 165 " --> pdb=" O PHE B 176 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 271 through 288 removed outlier: 5.607A pdb=" N LYS B 272 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL B 453 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL B 274 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE B 451 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASN B 276 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA B 449 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 447 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N SER B 443 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU B 284 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 441 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA B 286 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP B 439 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP B 405 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 414 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 408 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLY B 412 " --> pdb=" O VAL B 408 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 271 through 288 removed outlier: 5.607A pdb=" N LYS B 272 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL B 453 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL B 274 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE B 451 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASN B 276 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA B 449 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 447 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N SER B 443 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU B 284 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 441 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA B 286 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP B 439 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ASP B 448 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N TYR B 463 " --> pdb=" O ASP B 448 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU B 450 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE B 461 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU B 452 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 293 through 298 removed outlier: 3.503A pdb=" N GLN B 295 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N HIS B 338 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL B 422 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL B 336 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE B 335 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 348 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N CYS B 373 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 382 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 483 through 488 removed outlier: 3.670A pdb=" N GLY B 715 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 499 through 502 removed outlier: 4.873A pdb=" N LEU B 684 " --> pdb=" O VAL B 697 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 529 through 536 removed outlier: 6.903A pdb=" N SER B 520 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER B 532 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER B 518 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 534 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR B 516 " --> pdb=" O THR B 534 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE B 536 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASN B 514 " --> pdb=" O ILE B 536 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B 623 " --> pdb=" O LYS B 587 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS B 587 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY B 625 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE B 585 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU B 627 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N LEU B 583 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 529 through 536 removed outlier: 6.903A pdb=" N SER B 520 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER B 532 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER B 518 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 534 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR B 516 " --> pdb=" O THR B 534 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE B 536 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASN B 514 " --> pdb=" O ILE B 536 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LYS B 614 " --> pdb=" O GLY B 605 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY B 605 " --> pdb=" O LYS B 614 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR B 616 " --> pdb=" O LEU B 603 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 749 through 751 Processing sheet with id=AD9, first strand: chain 'B' and resid 780 through 798 removed outlier: 6.419A pdb=" N PHE B 788 " --> pdb=" O PRO B1160 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N MET B 790 " --> pdb=" O LEU B1158 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B1158 " --> pdb=" O MET B 790 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE B 792 " --> pdb=" O THR B1156 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR B1156 " --> pdb=" O ILE B 792 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU B1154 " --> pdb=" O PRO B 794 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR B 796 " --> pdb=" O LEU B1152 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU B1152 " --> pdb=" O TYR B 796 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLN B 798 " --> pdb=" O GLY B1150 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY B1150 " --> pdb=" O GLN B 798 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B1141 " --> pdb=" O THR B1156 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B1158 " --> pdb=" O HIS B1139 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS B1139 " --> pdb=" O LEU B1158 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AE2, first strand: chain 'B' and resid 1220 through 1223 removed outlier: 3.578A pdb=" N ALA B1179 " --> pdb=" O ILE B1223 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B1233 " --> pdb=" O CYS B1173 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1187 through 1190 Processing sheet with id=AE4, first strand: chain 'C' and resid 23 through 25 Processing sheet with id=AE5, first strand: chain 'C' and resid 47 through 48 Processing sheet with id=AE6, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AE7, first strand: chain 'C' and resid 180 through 184 removed outlier: 3.518A pdb=" N GLY C 165 " --> pdb=" O PHE C 176 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AE9, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AF1, first strand: chain 'C' and resid 270 through 288 removed outlier: 5.431A pdb=" N LYS C 272 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL C 453 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL C 274 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE C 451 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASN C 276 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA C 449 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C 447 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER C 443 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU C 284 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE C 441 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA C 286 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N TRP C 439 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP C 405 " --> pdb=" O THR C 401 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 414 " --> pdb=" O VAL C 406 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL C 408 " --> pdb=" O GLY C 412 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLY C 412 " --> pdb=" O VAL C 408 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 270 through 288 removed outlier: 5.431A pdb=" N LYS C 272 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL C 453 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL C 274 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE C 451 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASN C 276 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA C 449 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C 447 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER C 443 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU C 284 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE C 441 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA C 286 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N TRP C 439 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG C 460 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLN C 454 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 293 through 298 removed outlier: 3.545A pdb=" N ALA C 421 " --> pdb=" O HIS C 338 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 293 through 298 removed outlier: 3.545A pdb=" N ALA C 421 " --> pdb=" O HIS C 338 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N CYS C 373 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 483 through 488 removed outlier: 3.703A pdb=" N GLY C 715 " --> pdb=" O ALA C 707 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 499 through 502 removed outlier: 4.522A pdb=" N VAL C 694 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU C 684 " --> pdb=" O VAL C 697 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 529 through 536 removed outlier: 4.011A pdb=" N ALA C 531 " --> pdb=" O SER C 520 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 541 through 543 removed outlier: 3.864A pdb=" N PHE C 585 " --> pdb=" O GLY C 625 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY C 625 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS C 587 " --> pdb=" O THR C 623 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 510 through 521 current: chain 'C' and resid 564 through 569 Processing sheet with id=AF9, first strand: chain 'C' and resid 749 through 751 Processing sheet with id=AG1, first strand: chain 'C' and resid 780 through 798 removed outlier: 6.644A pdb=" N ASN C 781 " --> pdb=" O ILE C1167 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C1167 " --> pdb=" O ASN C 781 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER C 783 " --> pdb=" O ASP C1165 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP C1165 " --> pdb=" O SER C 783 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE C1163 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASN C 787 " --> pdb=" O GLY C1161 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE C1141 " --> pdb=" O THR C1156 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU C1158 " --> pdb=" O HIS C1139 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N HIS C1139 " --> pdb=" O LEU C1158 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 780 through 798 removed outlier: 6.644A pdb=" N ASN C 781 " --> pdb=" O ILE C1167 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C1167 " --> pdb=" O ASN C 781 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER C 783 " --> pdb=" O ASP C1165 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP C1165 " --> pdb=" O SER C 783 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE C1163 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASN C 787 " --> pdb=" O GLY C1161 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU C1189 " --> pdb=" O ILE C1169 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 804 through 806 Processing sheet with id=AG4, first strand: chain 'C' and resid 1220 through 1223 removed outlier: 3.856A pdb=" N ALA C1179 " --> pdb=" O ILE C1223 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C1178 " --> pdb=" O VAL C1174 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C1233 " --> pdb=" O CYS C1173 " (cutoff:3.500A) 1147 hydrogen bonds defined for protein. 3165 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.40 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9046 1.34 - 1.46: 7569 1.46 - 1.59: 12512 1.59 - 1.71: 0 1.71 - 1.83: 180 Bond restraints: 29307 Sorted by residual: bond pdb=" CA VAL F 123 " pdb=" CB VAL F 123 " ideal model delta sigma weight residual 1.527 1.550 -0.023 1.31e-02 5.83e+03 3.13e+00 bond pdb=" CB ARG C 981 " pdb=" CG ARG C 981 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.02e+00 bond pdb=" CB ARG B 981 " pdb=" CG ARG B 981 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.72e+00 bond pdb=" C GLU A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.69e+00 bond pdb=" CB THR B 853 " pdb=" CG2 THR B 853 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 ... (remaining 29302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 39310 2.34 - 4.67: 473 4.67 - 7.01: 36 7.01 - 9.35: 3 9.35 - 11.68: 2 Bond angle restraints: 39824 Sorted by residual: angle pdb=" C VAL A 638 " pdb=" N THR A 639 " pdb=" CA THR A 639 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.53e+01 angle pdb=" C2 NAG B1411 " pdb=" N2 NAG B1411 " pdb=" C7 NAG B1411 " ideal model delta sigma weight residual 124.56 136.24 -11.68 3.00e+00 1.11e-01 1.52e+01 angle pdb=" C2 NAG C1410 " pdb=" N2 NAG C1410 " pdb=" C7 NAG C1410 " ideal model delta sigma weight residual 124.56 136.17 -11.61 3.00e+00 1.11e-01 1.50e+01 angle pdb=" C ALA A 232 " pdb=" N ASN A 233 " pdb=" CA ASN A 233 " ideal model delta sigma weight residual 121.54 128.83 -7.29 1.91e+00 2.74e-01 1.46e+01 angle pdb=" N THR B 456 " pdb=" CA THR B 456 " pdb=" CB THR B 456 " ideal model delta sigma weight residual 114.17 109.93 4.24 1.14e+00 7.69e-01 1.38e+01 ... (remaining 39819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.64: 17302 23.64 - 47.29: 639 47.29 - 70.93: 95 70.93 - 94.57: 30 94.57 - 118.22: 5 Dihedral angle restraints: 18071 sinusoidal: 7631 harmonic: 10440 Sorted by residual: dihedral pdb=" CB CYS A 283 " pdb=" SG CYS A 283 " pdb=" SG CYS A 307 " pdb=" CB CYS A 307 " ideal model delta sinusoidal sigma weight residual 93.00 165.91 -72.91 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS C 649 " pdb=" SG CYS C 649 " pdb=" SG CYS C 700 " pdb=" CB CYS C 700 " ideal model delta sinusoidal sigma weight residual -86.00 -13.65 -72.35 1 1.00e+01 1.00e-02 6.69e+01 dihedral pdb=" CB CYS B 649 " pdb=" SG CYS B 649 " pdb=" SG CYS B 700 " pdb=" CB CYS B 700 " ideal model delta sinusoidal sigma weight residual -86.00 -18.65 -67.35 1 1.00e+01 1.00e-02 5.90e+01 ... (remaining 18068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3911 0.061 - 0.122: 733 0.122 - 0.183: 72 0.183 - 0.244: 6 0.244 - 0.305: 4 Chirality restraints: 4726 Sorted by residual: chirality pdb=" C2 NAG B1411 " pdb=" C1 NAG B1411 " pdb=" C3 NAG B1411 " pdb=" N2 NAG B1411 " both_signs ideal model delta sigma weight residual False -2.49 -2.19 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C2 NAG C1410 " pdb=" C1 NAG C1410 " pdb=" C3 NAG C1410 " pdb=" N2 NAG C1410 " both_signs ideal model delta sigma weight residual False -2.49 -2.19 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C1 NAG C1404 " pdb=" ND2 ASN C 726 " pdb=" C2 NAG C1404 " pdb=" O5 NAG C1404 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 4723 not shown) Planarity restraints: 5089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 98 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO A 99 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 572 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO C 573 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 573 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 573 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 374 " 0.012 2.00e-02 2.50e+03 1.47e-02 3.79e+00 pdb=" CG PHE B 374 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 374 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 374 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 374 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 374 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 374 " 0.000 2.00e-02 2.50e+03 ... (remaining 5086 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 14555 3.00 - 3.47: 26986 3.47 - 3.95: 47817 3.95 - 4.42: 54629 4.42 - 4.90: 90247 Nonbonded interactions: 234234 Sorted by model distance: nonbonded pdb=" O5 NAG M 1 " pdb=" O6 NAG M 1 " model vdw 2.520 2.432 nonbonded pdb=" O2 MAN J 5 " pdb=" O3 MAN J 5 " model vdw 2.542 2.432 nonbonded pdb=" O5 NAG M 2 " pdb=" O6 NAG M 2 " model vdw 2.567 2.432 nonbonded pdb=" O4 NAG I 2 " pdb=" O2 BMA I 3 " model vdw 2.575 2.432 nonbonded pdb=" O2 BMA J 3 " pdb=" O3 BMA J 3 " model vdw 2.586 2.432 ... (remaining 234229 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 26 through 128 or resid 147 through 1409 or resid 1411)) selection = (chain 'B' and (resid 26 through 58 or resid 64 through 112 or resid 119 through \ 128 or resid 147 through 356 or resid 369 through 426 or resid 435 through 880 \ or resid 894 through 904 or resid 915 through 970 or resid 972 through 989 or re \ sid 996 through 1014 or resid 1026 through 1231 or resid 1405 through 1413 or re \ sid 1415)) selection = (chain 'C' and (resid 26 through 58 or resid 64 through 112 or resid 119 through \ 128 or resid 147 through 356 or resid 369 through 426 or resid 435 through 880 \ or resid 894 through 904 or resid 915 through 970 or resid 972 through 989 or re \ sid 996 through 1014 or resid 1026 through 1231 or resid 1403 through 1411 or re \ sid 1413)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.330 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: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.160 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29419 Z= 0.170 Angle : 0.664 11.682 40110 Z= 0.337 Chirality : 0.048 0.305 4726 Planarity : 0.005 0.054 5046 Dihedral : 12.450 118.219 11245 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.14), residues: 3555 helix: 0.37 (0.20), residues: 629 sheet: -0.55 (0.16), residues: 1017 loop : -0.95 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 919 TYR 0.021 0.002 TYR A 606 PHE 0.032 0.002 PHE B 374 TRP 0.011 0.001 TRP B 439 HIS 0.007 0.001 HIS A 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (29307) covalent geometry : angle 0.63959 / 0.33 (39824) SS BOND : bond 0.00288 / 0.19 ( 50) SS BOND : angle 1.59052 / 1.12 ( 100) hydrogen bonds : bond 0.18534 / 12.62 ( 1039) hydrogen bonds : angle 8.85361 / 6.17 ( 3165) link_ALPHA1-3 : bond 0.00693 / 0.35 ( 3) link_ALPHA1-3 : angle 1.33373 / 0.73 ( 9) link_ALPHA1-6 : bond 0.01105 / 0.56 ( 3) link_ALPHA1-6 : angle 1.94841 / 1.09 ( 9) link_BETA1-4 : bond 0.00296 / 0.17 ( 13) link_BETA1-4 : angle 2.11296 / 1.35 ( 39) link_NAG-ASN : bond 0.00424 / 0.31 ( 43) link_NAG-ASN : angle 2.67012 / 1.75 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 HIS cc_start: 0.8017 (t70) cc_final: 0.7604 (m170) REVERT: F 102 MET cc_start: 0.5920 (mmp) cc_final: 0.5381 (mmt) REVERT: B 939 MET cc_start: 0.8834 (mtm) cc_final: 0.8463 (mtm) REVERT: C 967 THR cc_start: 0.6684 (p) cc_final: 0.6458 (t) REVERT: C 1240 ASP cc_start: 0.7317 (t70) cc_final: 0.7054 (m-30) outliers start: 0 outliers final: 1 residues processed: 422 average time/residue: 0.5788 time to fit residues: 292.1527 Evaluate side-chains 240 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1075 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0020 chunk 298 optimal weight: 1.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 HIS ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN B 71 HIS B 89 HIS B 979 GLN B 996 GLN B1061 GLN B1128 GLN C 270 HIS C 301 GLN C 308 ASN C 771 GLN C1117 GLN C1128 GLN C1149 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.152902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.116663 restraints weight = 38813.119| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.70 r_work: 0.3177 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29419 Z= 0.145 Angle : 0.577 9.704 40110 Z= 0.292 Chirality : 0.044 0.262 4726 Planarity : 0.004 0.048 5046 Dihedral : 7.587 99.561 5233 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.07 % Allowed : 5.98 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3555 helix: 1.11 (0.20), residues: 640 sheet: -0.50 (0.16), residues: 1021 loop : -0.88 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 33 TYR 0.016 0.001 TYR G 69 PHE 0.013 0.001 PHE B 91 TRP 0.009 0.001 TRP F 55 HIS 0.008 0.001 HIS B 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (29307) covalent geometry : angle 0.55561 / 0.29 (39824) SS BOND : bond 0.00231 / 0.15 ( 50) SS BOND : angle 1.43299 / 1.00 ( 100) hydrogen bonds : bond 0.04115 / 2.81 ( 1039) hydrogen bonds : angle 6.08473 / 4.30 ( 3165) link_ALPHA1-3 : bond 0.00604 / 0.30 ( 3) link_ALPHA1-3 : angle 1.46994 / 0.81 ( 9) link_ALPHA1-6 : bond 0.01199 / 0.60 ( 3) link_ALPHA1-6 : angle 2.14124 / 1.25 ( 9) link_BETA1-4 : bond 0.00230 / 0.15 ( 13) link_BETA1-4 : angle 2.01872 / 1.28 ( 39) link_NAG-ASN : bond 0.00307 / 0.22 ( 43) link_NAG-ASN : angle 2.24136 / 1.44 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 273 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 HIS cc_start: 0.8643 (t70) cc_final: 0.8310 (m170) REVERT: A 851 MET cc_start: 0.8688 (ttt) cc_final: 0.8448 (ttt) REVERT: A 1040 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: A 1076 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6894 (mt) REVERT: F 89 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.5720 (tmm) REVERT: F 102 MET cc_start: 0.6973 (mmp) cc_final: 0.6033 (mmt) REVERT: B 34 ARG cc_start: 0.7173 (mtp-110) cc_final: 0.6800 (mtp85) REVERT: B 332 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: B 371 TYR cc_start: 0.7617 (m-80) cc_final: 0.7193 (m-80) REVERT: B 433 ASP cc_start: 0.7034 (t0) cc_final: 0.6753 (p0) REVERT: B 490 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6453 (mpt-90) REVERT: B 939 MET cc_start: 0.9114 (mtm) cc_final: 0.8714 (mtm) REVERT: B 1165 ASP cc_start: 0.8355 (m-30) cc_final: 0.8076 (m-30) REVERT: C 34 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.6227 (mtm110) REVERT: C 35 PHE cc_start: 0.7356 (t80) cc_final: 0.6609 (t80) REVERT: C 42 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: C 228 GLN cc_start: 0.6710 (tt0) cc_final: 0.6269 (tm-30) REVERT: C 452 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: C 460 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7900 (ptm160) REVERT: C 594 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8270 (tt) REVERT: C 946 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7150 (p0) REVERT: C 1113 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8612 (mtpm) REVERT: C 1209 MET cc_start: 0.8406 (mtt) cc_final: 0.8165 (mtt) REVERT: C 1235 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6227 (ttm110) REVERT: C 1240 ASP cc_start: 0.7937 (t70) cc_final: 0.6969 (m-30) outliers start: 64 outliers final: 27 residues processed: 309 average time/residue: 0.5815 time to fit residues: 217.1225 Evaluate side-chains 279 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1040 GLU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 460 ARG Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 817 SER Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 946 ASP Chi-restraints excluded: chain C residue 1077 LEU Chi-restraints excluded: chain C residue 1113 LYS Chi-restraints excluded: chain C residue 1217 VAL Chi-restraints excluded: chain C residue 1235 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 309 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 329 optimal weight: 2.9990 chunk 277 optimal weight: 0.5980 chunk 111 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 300 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 HIS B 71 HIS B 89 HIS B1055 GLN C 270 HIS C 300 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.151498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114055 restraints weight = 38357.513| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.42 r_work: 0.3168 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29419 Z= 0.156 Angle : 0.568 9.581 40110 Z= 0.286 Chirality : 0.044 0.257 4726 Planarity : 0.004 0.042 5046 Dihedral : 7.206 83.721 5231 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.23 % Allowed : 7.66 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.14), residues: 3555 helix: 1.39 (0.21), residues: 639 sheet: -0.51 (0.16), residues: 1069 loop : -0.86 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 33 TYR 0.015 0.001 TYR A 676 PHE 0.015 0.001 PHE A 296 TRP 0.006 0.001 TRP F 55 HIS 0.014 0.001 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (29307) covalent geometry : angle 0.54603 / 0.28 (39824) SS BOND : bond 0.00231 / 0.16 ( 50) SS BOND : angle 1.43074 / 0.96 ( 100) hydrogen bonds : bond 0.03952 / 2.72 ( 1039) hydrogen bonds : angle 5.65656 / 4.01 ( 3165) link_ALPHA1-3 : bond 0.00527 / 0.26 ( 3) link_ALPHA1-3 : angle 1.45357 / 0.78 ( 9) link_ALPHA1-6 : bond 0.01304 / 0.65 ( 3) link_ALPHA1-6 : angle 2.47508 / 1.42 ( 9) link_BETA1-4 : bond 0.00257 / 0.17 ( 13) link_BETA1-4 : angle 2.03400 / 1.29 ( 39) link_NAG-ASN : bond 0.00264 / 0.18 ( 43) link_NAG-ASN : angle 2.20481 / 1.38 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 252 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 SER cc_start: 0.8184 (t) cc_final: 0.7968 (m) REVERT: A 164 VAL cc_start: 0.7965 (p) cc_final: 0.7754 (t) REVERT: A 270 HIS cc_start: 0.8598 (t70) cc_final: 0.8279 (m170) REVERT: A 660 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: A 1040 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7871 (tp30) REVERT: A 1076 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6896 (mt) REVERT: F 89 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.5957 (tmm) REVERT: F 102 MET cc_start: 0.6913 (mmp) cc_final: 0.5940 (mmt) REVERT: B 332 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: B 371 TYR cc_start: 0.7524 (m-80) cc_final: 0.7201 (m-80) REVERT: B 386 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8300 (mtpp) REVERT: B 433 ASP cc_start: 0.7055 (t0) cc_final: 0.6740 (p0) REVERT: B 490 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6422 (mpt-90) REVERT: B 679 ASP cc_start: 0.8258 (p0) cc_final: 0.8057 (p0) REVERT: B 924 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7966 (mtm110) REVERT: B 939 MET cc_start: 0.9113 (mtm) cc_final: 0.8746 (mtm) REVERT: B 1165 ASP cc_start: 0.8405 (m-30) cc_final: 0.8118 (m-30) REVERT: C 35 PHE cc_start: 0.7436 (t80) cc_final: 0.6634 (t80) REVERT: C 42 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: C 191 ARG cc_start: 0.7111 (tpp-160) cc_final: 0.6679 (mmm160) REVERT: C 228 GLN cc_start: 0.6698 (tt0) cc_final: 0.6224 (tm-30) REVERT: C 452 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: C 460 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7933 (ptm160) REVERT: C 594 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8336 (tt) REVERT: C 1113 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8599 (mtpm) REVERT: C 1209 MET cc_start: 0.8511 (mtt) cc_final: 0.8276 (mtt) REVERT: C 1235 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6246 (ttm110) REVERT: C 1240 ASP cc_start: 0.7884 (t70) cc_final: 0.6919 (m-30) outliers start: 69 outliers final: 32 residues processed: 294 average time/residue: 0.5646 time to fit residues: 199.6671 Evaluate side-chains 280 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 235 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1040 GLU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1040 GLU Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 460 ARG Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 817 SER Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 948 GLU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1077 LEU Chi-restraints excluded: chain C residue 1113 LYS Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1235 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 343 optimal weight: 1.9990 chunk 262 optimal weight: 0.9980 chunk 278 optimal weight: 1.9990 chunk 350 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 277 optimal weight: 0.7980 chunk 315 optimal weight: 0.0770 chunk 226 optimal weight: 0.8980 chunk 182 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 310 optimal weight: 3.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 996 GLN B 71 HIS B1039 GLN B1043 ASN C 270 HIS C 300 ASN C 705 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.152500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115306 restraints weight = 38415.698| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.42 r_work: 0.3189 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29419 Z= 0.116 Angle : 0.538 9.568 40110 Z= 0.268 Chirality : 0.043 0.252 4726 Planarity : 0.003 0.052 5046 Dihedral : 6.725 64.055 5231 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.20 % Allowed : 8.69 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3555 helix: 1.63 (0.21), residues: 640 sheet: -0.46 (0.16), residues: 1024 loop : -0.86 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 33 TYR 0.028 0.001 TYR B 237 PHE 0.012 0.001 PHE C 183 TRP 0.007 0.001 TRP F 55 HIS 0.016 0.001 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (29307) covalent geometry : angle 0.51434 / 0.26 (39824) SS BOND : bond 0.00188 / 0.13 ( 50) SS BOND : angle 1.26278 / 0.85 ( 100) hydrogen bonds : bond 0.03518 / 2.41 ( 1039) hydrogen bonds : angle 5.33974 / 3.80 ( 3165) link_ALPHA1-3 : bond 0.00710 / 0.36 ( 3) link_ALPHA1-3 : angle 1.35456 / 0.75 ( 9) link_ALPHA1-6 : bond 0.01293 / 0.65 ( 3) link_ALPHA1-6 : angle 2.38471 / 1.37 ( 9) link_BETA1-4 : bond 0.00244 / 0.15 ( 13) link_BETA1-4 : angle 1.85375 / 1.19 ( 39) link_NAG-ASN : bond 0.00327 / 0.23 ( 43) link_NAG-ASN : angle 2.33126 / 1.53 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 248 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8158 (ttm-80) cc_final: 0.7946 (ttm-80) REVERT: A 164 VAL cc_start: 0.8121 (p) cc_final: 0.7869 (t) REVERT: A 270 HIS cc_start: 0.8624 (t70) cc_final: 0.8288 (m170) REVERT: A 660 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: A 824 THR cc_start: 0.8494 (p) cc_final: 0.8095 (p) REVERT: A 851 MET cc_start: 0.8670 (ttt) cc_final: 0.8423 (ttt) REVERT: A 1076 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6769 (mt) REVERT: F 53 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7050 (tp) REVERT: F 89 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6543 (tmt) REVERT: F 102 MET cc_start: 0.6851 (mmp) cc_final: 0.5975 (mmt) REVERT: B 89 HIS cc_start: 0.5733 (m90) cc_final: 0.5171 (m170) REVERT: B 332 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: B 371 TYR cc_start: 0.7592 (m-80) cc_final: 0.7275 (m-80) REVERT: B 433 ASP cc_start: 0.7013 (t0) cc_final: 0.6716 (p0) REVERT: B 490 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6373 (mpt-90) REVERT: B 924 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.7999 (mtm110) REVERT: B 939 MET cc_start: 0.9104 (mtm) cc_final: 0.8643 (mtm) REVERT: B 1165 ASP cc_start: 0.8428 (m-30) cc_final: 0.8160 (m-30) REVERT: C 34 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.6243 (mtm110) REVERT: C 35 PHE cc_start: 0.7238 (t80) cc_final: 0.6491 (t80) REVERT: C 42 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: C 191 ARG cc_start: 0.7185 (tpp-160) cc_final: 0.6750 (mmm160) REVERT: C 228 GLN cc_start: 0.6658 (tt0) cc_final: 0.6164 (tm-30) REVERT: C 452 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: C 460 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7887 (ptm160) REVERT: C 594 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8336 (tt) REVERT: C 682 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7448 (mt0) REVERT: C 758 LYS cc_start: 0.8894 (ttpp) cc_final: 0.8385 (ttmm) REVERT: C 1113 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8578 (mtpm) REVERT: C 1209 MET cc_start: 0.8450 (mtt) cc_final: 0.8216 (mtt) REVERT: C 1235 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6498 (ttm110) REVERT: C 1240 ASP cc_start: 0.7839 (t70) cc_final: 0.6886 (m-30) outliers start: 68 outliers final: 31 residues processed: 288 average time/residue: 0.5991 time to fit residues: 207.2813 Evaluate side-chains 274 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 460 ARG Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 682 GLN Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1077 LEU Chi-restraints excluded: chain C residue 1113 LYS Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1217 VAL Chi-restraints excluded: chain C residue 1235 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 99 optimal weight: 1.9990 chunk 312 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 313 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 258 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 GLN A 814 ASN A 996 GLN B 71 HIS B 106 GLN B 170 ASN B 282 ASN B 849 ASN C 270 HIS C 300 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.148370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.111924 restraints weight = 38762.609| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.74 r_work: 0.3103 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 29419 Z= 0.255 Angle : 0.654 10.751 40110 Z= 0.327 Chirality : 0.048 0.281 4726 Planarity : 0.004 0.052 5046 Dihedral : 7.416 57.595 5231 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.68 % Allowed : 9.18 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.14), residues: 3555 helix: 1.17 (0.20), residues: 655 sheet: -0.46 (0.16), residues: 1021 loop : -0.98 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 33 TYR 0.029 0.002 TYR B 237 PHE 0.021 0.002 PHE A 411 TRP 0.008 0.001 TRP B 259 HIS 0.017 0.002 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.26 (29307) covalent geometry : angle 0.62690 / 0.32 (39824) SS BOND : bond 0.00331 / 0.22 ( 50) SS BOND : angle 1.60283 / 1.10 ( 100) hydrogen bonds : bond 0.04402 / 3.04 ( 1039) hydrogen bonds : angle 5.59129 / 3.96 ( 3165) link_ALPHA1-3 : bond 0.00390 / 0.19 ( 3) link_ALPHA1-3 : angle 1.76038 / 0.91 ( 9) link_ALPHA1-6 : bond 0.01087 / 0.55 ( 3) link_ALPHA1-6 : angle 2.34476 / 1.29 ( 9) link_BETA1-4 : bond 0.00344 / 0.21 ( 13) link_BETA1-4 : angle 2.36554 / 1.49 ( 39) link_NAG-ASN : bond 0.00484 / 0.35 ( 43) link_NAG-ASN : angle 2.70761 / 1.75 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 247 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7918 (t) REVERT: A 270 HIS cc_start: 0.8642 (t70) cc_final: 0.8297 (m170) REVERT: A 660 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: A 924 ARG cc_start: 0.8269 (mmp80) cc_final: 0.7363 (mtm110) REVERT: A 1076 ILE cc_start: 0.7221 (OUTLIER) cc_final: 0.6967 (mt) REVERT: F 89 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6217 (tmt) REVERT: F 102 MET cc_start: 0.6717 (mmp) cc_final: 0.5834 (mmt) REVERT: B 332 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: B 371 TYR cc_start: 0.7640 (m-80) cc_final: 0.7355 (m-80) REVERT: B 386 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8344 (mtpp) REVERT: B 433 ASP cc_start: 0.7215 (t0) cc_final: 0.6722 (p0) REVERT: B 490 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6523 (tpt-90) REVERT: B 924 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.8001 (mtm110) REVERT: B 939 MET cc_start: 0.9124 (mtm) cc_final: 0.8764 (mtm) REVERT: B 1165 ASP cc_start: 0.8516 (m-30) cc_final: 0.8245 (m-30) REVERT: B 1234 THR cc_start: 0.7637 (m) cc_final: 0.7249 (p) REVERT: C 34 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.6263 (mtm110) REVERT: C 35 PHE cc_start: 0.7386 (t80) cc_final: 0.6622 (t80) REVERT: C 42 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7241 (mp10) REVERT: C 191 ARG cc_start: 0.7127 (tpp-160) cc_final: 0.6814 (mmm160) REVERT: C 228 GLN cc_start: 0.6585 (tt0) cc_final: 0.6113 (tm-30) REVERT: C 452 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: C 460 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8066 (ptm160) REVERT: C 592 THR cc_start: 0.8573 (m) cc_final: 0.8347 (p) REVERT: C 682 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7489 (mt0) REVERT: C 967 THR cc_start: 0.6891 (p) cc_final: 0.6483 (t) REVERT: C 1113 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8629 (mtpm) REVERT: C 1235 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6330 (ttm110) REVERT: C 1240 ASP cc_start: 0.7942 (t70) cc_final: 0.6910 (m-30) outliers start: 83 outliers final: 47 residues processed: 303 average time/residue: 0.6039 time to fit residues: 220.2167 Evaluate side-chains 289 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 228 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1040 GLU Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 460 ARG Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 682 GLN Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 817 SER Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 948 GLU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1077 LEU Chi-restraints excluded: chain C residue 1113 LYS Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1217 VAL Chi-restraints excluded: chain C residue 1235 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 154 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 313 optimal weight: 3.9990 chunk 304 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 186 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 343 optimal weight: 0.6980 chunk 239 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 996 GLN B 71 HIS B 282 ASN B 771 GLN C 270 HIS C 300 ASN C 849 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.150321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114108 restraints weight = 38744.531| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.72 r_work: 0.3137 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29419 Z= 0.139 Angle : 0.562 10.192 40110 Z= 0.282 Chirality : 0.044 0.311 4726 Planarity : 0.004 0.048 5046 Dihedral : 6.909 58.269 5231 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.62 % Allowed : 9.83 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3555 helix: 1.41 (0.20), residues: 657 sheet: -0.50 (0.16), residues: 1030 loop : -0.93 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 33 TYR 0.024 0.001 TYR B 237 PHE 0.020 0.001 PHE A 185 TRP 0.008 0.001 TRP F 55 HIS 0.009 0.001 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (29307) covalent geometry : angle 0.53676 / 0.28 (39824) SS BOND : bond 0.00252 / 0.16 ( 50) SS BOND : angle 1.40847 / 0.98 ( 100) hydrogen bonds : bond 0.03658 / 2.52 ( 1039) hydrogen bonds : angle 5.29007 / 3.76 ( 3165) link_ALPHA1-3 : bond 0.00714 / 0.36 ( 3) link_ALPHA1-3 : angle 1.37629 / 0.75 ( 9) link_ALPHA1-6 : bond 0.01144 / 0.58 ( 3) link_ALPHA1-6 : angle 1.71636 / 1.01 ( 9) link_BETA1-4 : bond 0.00260 / 0.16 ( 13) link_BETA1-4 : angle 1.94838 / 1.24 ( 39) link_NAG-ASN : bond 0.00371 / 0.27 ( 43) link_NAG-ASN : angle 2.48959 / 1.62 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 242 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 HIS cc_start: 0.8660 (t70) cc_final: 0.8301 (m170) REVERT: A 660 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: A 824 THR cc_start: 0.8595 (p) cc_final: 0.8197 (p) REVERT: A 851 MET cc_start: 0.8727 (ttt) cc_final: 0.8471 (ttt) REVERT: A 924 ARG cc_start: 0.8225 (mmp80) cc_final: 0.7378 (mtm110) REVERT: A 1076 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6842 (mt) REVERT: F 53 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.6859 (tp) REVERT: F 89 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6590 (tmt) REVERT: F 102 MET cc_start: 0.6608 (mmp) cc_final: 0.5753 (mmt) REVERT: B 332 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: B 371 TYR cc_start: 0.7591 (m-80) cc_final: 0.7326 (m-80) REVERT: B 433 ASP cc_start: 0.7052 (t0) cc_final: 0.6669 (p0) REVERT: B 490 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6468 (tpt-90) REVERT: B 543 CYS cc_start: 0.7148 (t) cc_final: 0.6946 (t) REVERT: B 924 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.7985 (mtm110) REVERT: B 939 MET cc_start: 0.9095 (mtm) cc_final: 0.8695 (mtm) REVERT: B 1165 ASP cc_start: 0.8488 (m-30) cc_final: 0.8207 (m-30) REVERT: C 34 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.6277 (mtm110) REVERT: C 35 PHE cc_start: 0.7370 (t80) cc_final: 0.6569 (t80) REVERT: C 42 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7188 (mp10) REVERT: C 191 ARG cc_start: 0.7136 (tpp-160) cc_final: 0.6831 (mmm160) REVERT: C 228 GLN cc_start: 0.6652 (tt0) cc_final: 0.6115 (tm-30) REVERT: C 452 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: C 460 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7895 (ptm160) REVERT: C 592 THR cc_start: 0.8492 (m) cc_final: 0.8213 (p) REVERT: C 682 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7416 (mt0) REVERT: C 967 THR cc_start: 0.6933 (p) cc_final: 0.6516 (t) REVERT: C 1113 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8612 (mtpm) REVERT: C 1162 ASP cc_start: 0.7750 (m-30) cc_final: 0.7295 (t70) REVERT: C 1235 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6257 (ttm110) REVERT: C 1240 ASP cc_start: 0.7904 (t70) cc_final: 0.6926 (m-30) outliers start: 81 outliers final: 42 residues processed: 289 average time/residue: 0.6000 time to fit residues: 208.8514 Evaluate side-chains 284 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 460 ARG Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 682 GLN Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 817 SER Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 929 LEU Chi-restraints excluded: chain C residue 948 GLU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1077 LEU Chi-restraints excluded: chain C residue 1113 LYS Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1217 VAL Chi-restraints excluded: chain C residue 1235 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 72 optimal weight: 0.4980 chunk 116 optimal weight: 0.1980 chunk 96 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 240 optimal weight: 0.6980 chunk 246 optimal weight: 6.9990 chunk 276 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 343 optimal weight: 0.8980 chunk 330 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 996 GLN B 71 HIS C 270 HIS C 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.151729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114254 restraints weight = 38429.493| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.45 r_work: 0.3167 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29419 Z= 0.111 Angle : 0.532 9.482 40110 Z= 0.267 Chirality : 0.043 0.262 4726 Planarity : 0.004 0.050 5046 Dihedral : 6.539 59.939 5231 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.17 % Allowed : 10.86 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3555 helix: 1.66 (0.20), residues: 655 sheet: -0.45 (0.16), residues: 1026 loop : -0.90 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 314 TYR 0.025 0.001 TYR B 237 PHE 0.018 0.001 PHE C 39 TRP 0.008 0.001 TRP F 55 HIS 0.007 0.001 HIS B 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (29307) covalent geometry : angle 0.50959 / 0.26 (39824) SS BOND : bond 0.00199 / 0.13 ( 50) SS BOND : angle 1.25320 / 0.86 ( 100) hydrogen bonds : bond 0.03364 / 2.31 ( 1039) hydrogen bonds : angle 5.06442 / 3.60 ( 3165) link_ALPHA1-3 : bond 0.00787 / 0.40 ( 3) link_ALPHA1-3 : angle 1.37492 / 0.76 ( 9) link_ALPHA1-6 : bond 0.00949 / 0.49 ( 3) link_ALPHA1-6 : angle 1.44339 / 0.87 ( 9) link_BETA1-4 : bond 0.00273 / 0.17 ( 13) link_BETA1-4 : angle 1.84199 / 1.19 ( 39) link_NAG-ASN : bond 0.00366 / 0.26 ( 43) link_NAG-ASN : angle 2.29054 / 1.50 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 234 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8149 (ttm-80) cc_final: 0.7621 (ttp80) REVERT: A 270 HIS cc_start: 0.8612 (t70) cc_final: 0.8297 (m170) REVERT: A 824 THR cc_start: 0.8472 (p) cc_final: 0.8057 (p) REVERT: A 924 ARG cc_start: 0.8175 (mmp80) cc_final: 0.7287 (mtm110) REVERT: F 53 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.6677 (tp) REVERT: F 89 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6497 (tmt) REVERT: F 102 MET cc_start: 0.6657 (mmp) cc_final: 0.5815 (mmt) REVERT: B 89 HIS cc_start: 0.5730 (m90) cc_final: 0.5015 (m170) REVERT: B 490 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6559 (mpt-90) REVERT: B 543 CYS cc_start: 0.7109 (t) cc_final: 0.6891 (t) REVERT: B 924 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.8013 (mtm110) REVERT: B 939 MET cc_start: 0.9079 (mtm) cc_final: 0.8671 (mtm) REVERT: B 1165 ASP cc_start: 0.8418 (m-30) cc_final: 0.8145 (m-30) REVERT: C 34 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.6277 (mtm110) REVERT: C 35 PHE cc_start: 0.7324 (t80) cc_final: 0.6544 (t80) REVERT: C 42 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7278 (mp10) REVERT: C 191 ARG cc_start: 0.7142 (tpp-160) cc_final: 0.6850 (mmm160) REVERT: C 228 GLN cc_start: 0.6672 (tt0) cc_final: 0.6199 (tm-30) REVERT: C 452 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: C 460 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7826 (ptm160) REVERT: C 466 ASP cc_start: 0.8174 (p0) cc_final: 0.7889 (p0) REVERT: C 594 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8428 (tt) REVERT: C 682 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7367 (mt0) REVERT: C 967 THR cc_start: 0.7105 (p) cc_final: 0.6678 (t) REVERT: C 998 LEU cc_start: 0.7431 (mm) cc_final: 0.7168 (tp) REVERT: C 1113 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8592 (mtpm) REVERT: C 1162 ASP cc_start: 0.7572 (m-30) cc_final: 0.7203 (t70) REVERT: C 1240 ASP cc_start: 0.7851 (t70) cc_final: 0.6939 (m-30) outliers start: 67 outliers final: 40 residues processed: 277 average time/residue: 0.5862 time to fit residues: 196.1474 Evaluate side-chains 272 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 460 ARG Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 682 GLN Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 817 SER Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 948 GLU Chi-restraints excluded: chain C residue 1077 LEU Chi-restraints excluded: chain C residue 1113 LYS Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1217 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 327 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 227 optimal weight: 0.0070 chunk 61 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 996 GLN B 71 HIS B 110 HIS B 282 ASN B 459 GLN ** B1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS C 300 ASN C 571 ASN C1222 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.147952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110093 restraints weight = 38517.681| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.45 r_work: 0.3113 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 29419 Z= 0.255 Angle : 0.648 11.635 40110 Z= 0.325 Chirality : 0.048 0.352 4726 Planarity : 0.004 0.060 5046 Dihedral : 7.260 59.698 5231 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.59 % Allowed : 10.70 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3555 helix: 1.26 (0.20), residues: 656 sheet: -0.49 (0.16), residues: 1027 loop : -0.99 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 33 TYR 0.021 0.002 TYR B 237 PHE 0.022 0.002 PHE A 411 TRP 0.008 0.001 TRP B 259 HIS 0.008 0.001 HIS B 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.26 (29307) covalent geometry : angle 0.62108 / 0.32 (39824) SS BOND : bond 0.00331 / 0.22 ( 50) SS BOND : angle 1.62842 / 1.12 ( 100) hydrogen bonds : bond 0.04310 / 2.97 ( 1039) hydrogen bonds : angle 5.42555 / 3.84 ( 3165) link_ALPHA1-3 : bond 0.00462 / 0.23 ( 3) link_ALPHA1-3 : angle 1.73955 / 0.88 ( 9) link_ALPHA1-6 : bond 0.00726 / 0.37 ( 3) link_ALPHA1-6 : angle 1.84337 / 1.04 ( 9) link_BETA1-4 : bond 0.00364 / 0.23 ( 13) link_BETA1-4 : angle 2.35450 / 1.48 ( 39) link_NAG-ASN : bond 0.00498 / 0.36 ( 43) link_NAG-ASN : angle 2.71994 / 1.77 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 227 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7865 (ttm-80) REVERT: A 270 HIS cc_start: 0.8612 (t70) cc_final: 0.8292 (m170) REVERT: A 924 ARG cc_start: 0.8330 (mmp80) cc_final: 0.7825 (tpp80) REVERT: F 53 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.6456 (tp) REVERT: F 89 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.5924 (tmm) REVERT: F 102 MET cc_start: 0.6691 (mmp) cc_final: 0.5933 (mmt) REVERT: B 490 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6525 (tpt-90) REVERT: B 924 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7958 (mtm110) REVERT: B 939 MET cc_start: 0.9129 (mtm) cc_final: 0.8728 (mtm) REVERT: B 979 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: B 1165 ASP cc_start: 0.8468 (m-30) cc_final: 0.8218 (m-30) REVERT: B 1234 THR cc_start: 0.7675 (m) cc_final: 0.7295 (p) REVERT: C 34 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.6288 (mtm110) REVERT: C 35 PHE cc_start: 0.7351 (t80) cc_final: 0.6602 (t80) REVERT: C 42 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7290 (mp10) REVERT: C 191 ARG cc_start: 0.7171 (tpp-160) cc_final: 0.6846 (mmm160) REVERT: C 228 GLN cc_start: 0.6556 (tt0) cc_final: 0.5999 (tm-30) REVERT: C 452 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: C 460 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7987 (ptm160) REVERT: C 592 THR cc_start: 0.8592 (m) cc_final: 0.8349 (p) REVERT: C 682 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7471 (mt0) REVERT: C 967 THR cc_start: 0.6817 (p) cc_final: 0.6426 (t) REVERT: C 1113 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8588 (mtpm) REVERT: C 1162 ASP cc_start: 0.7741 (m-30) cc_final: 0.7319 (t70) REVERT: C 1222 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8071 (tm130) REVERT: C 1235 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6407 (ttm110) REVERT: C 1240 ASP cc_start: 0.7909 (t70) cc_final: 0.6923 (m-30) outliers start: 80 outliers final: 54 residues processed: 282 average time/residue: 0.5800 time to fit residues: 198.4927 Evaluate side-chains 290 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 224 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1183 ARG Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 979 GLN Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 460 ARG Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 682 GLN Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 802 THR Chi-restraints excluded: chain C residue 817 SER Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 948 GLU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1077 LEU Chi-restraints excluded: chain C residue 1113 LYS Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1217 VAL Chi-restraints excluded: chain C residue 1222 GLN Chi-restraints excluded: chain C residue 1235 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 208 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 292 optimal weight: 0.8980 chunk 203 optimal weight: 0.0870 chunk 231 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 163 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 chunk 105 optimal weight: 0.3980 chunk 334 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 HIS B 282 ASN B 825 GLN C 270 HIS C 300 ASN C 571 ASN C1222 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.151420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114144 restraints weight = 38457.537| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.46 r_work: 0.3166 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29419 Z= 0.102 Angle : 0.540 9.672 40110 Z= 0.272 Chirality : 0.044 0.271 4726 Planarity : 0.004 0.054 5046 Dihedral : 6.594 59.367 5231 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.75 % Allowed : 11.86 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3555 helix: 1.63 (0.20), residues: 655 sheet: -0.53 (0.16), residues: 1022 loop : -0.89 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 33 TYR 0.023 0.001 TYR B 237 PHE 0.021 0.001 PHE C 39 TRP 0.011 0.001 TRP F 55 HIS 0.006 0.001 HIS B 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (29307) covalent geometry : angle 0.51772 / 0.27 (39824) SS BOND : bond 0.00219 / 0.14 ( 50) SS BOND : angle 1.29947 / 0.87 ( 100) hydrogen bonds : bond 0.03385 / 2.31 ( 1039) hydrogen bonds : angle 5.08147 / 3.61 ( 3165) link_ALPHA1-3 : bond 0.00910 / 0.46 ( 3) link_ALPHA1-3 : angle 1.23323 / 0.69 ( 9) link_ALPHA1-6 : bond 0.01119 / 0.57 ( 3) link_ALPHA1-6 : angle 1.38953 / 0.85 ( 9) link_BETA1-4 : bond 0.00276 / 0.17 ( 13) link_BETA1-4 : angle 1.79330 / 1.15 ( 39) link_NAG-ASN : bond 0.00427 / 0.31 ( 43) link_NAG-ASN : angle 2.35149 / 1.55 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 231 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 HIS cc_start: 0.8615 (t70) cc_final: 0.8279 (m170) REVERT: A 821 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7884 (mt0) REVERT: A 824 THR cc_start: 0.8479 (p) cc_final: 0.8044 (p) REVERT: A 924 ARG cc_start: 0.8328 (mmp80) cc_final: 0.7849 (tpp80) REVERT: F 53 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.6436 (tp) REVERT: F 89 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6667 (tmt) REVERT: F 102 MET cc_start: 0.6689 (mmp) cc_final: 0.5920 (mmt) REVERT: B 89 HIS cc_start: 0.5751 (m90) cc_final: 0.4945 (m170) REVERT: B 490 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6448 (tpt-90) REVERT: B 543 CYS cc_start: 0.7088 (t) cc_final: 0.6874 (t) REVERT: B 924 ARG cc_start: 0.8246 (mtm-85) cc_final: 0.7987 (mtm110) REVERT: B 939 MET cc_start: 0.9064 (mtm) cc_final: 0.8673 (mtm) REVERT: B 979 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: B 1165 ASP cc_start: 0.8425 (m-30) cc_final: 0.8155 (m-30) REVERT: C 34 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.6250 (mtm110) REVERT: C 35 PHE cc_start: 0.7347 (t80) cc_final: 0.6602 (t80) REVERT: C 42 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7241 (mp10) REVERT: C 191 ARG cc_start: 0.7133 (tpp-160) cc_final: 0.6837 (mmm160) REVERT: C 228 GLN cc_start: 0.6642 (tt0) cc_final: 0.6167 (tm-30) REVERT: C 452 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: C 460 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7861 (ptm160) REVERT: C 592 THR cc_start: 0.8519 (m) cc_final: 0.8272 (p) REVERT: C 594 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8426 (tt) REVERT: C 967 THR cc_start: 0.7178 (p) cc_final: 0.6742 (t) REVERT: C 998 LEU cc_start: 0.7467 (mm) cc_final: 0.7159 (tp) REVERT: C 1113 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8575 (mtpm) REVERT: C 1162 ASP cc_start: 0.7655 (m-30) cc_final: 0.7287 (t70) REVERT: C 1235 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6436 (ttm110) REVERT: C 1240 ASP cc_start: 0.7770 (t70) cc_final: 0.6910 (m-30) outliers start: 54 outliers final: 36 residues processed: 268 average time/residue: 0.5832 time to fit residues: 188.9540 Evaluate side-chains 274 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 979 GLN Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 460 ARG Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 682 GLN Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 948 GLU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1077 LEU Chi-restraints excluded: chain C residue 1113 LYS Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1235 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 56 optimal weight: 0.0470 chunk 150 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 174 optimal weight: 0.6980 chunk 350 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 331 optimal weight: 2.9990 chunk 345 optimal weight: 3.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 HIS B 825 GLN C 270 HIS C 300 ASN C 571 ASN C1222 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.149782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112223 restraints weight = 38186.076| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.43 r_work: 0.3139 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29419 Z= 0.165 Angle : 0.574 10.748 40110 Z= 0.288 Chirality : 0.045 0.264 4726 Planarity : 0.004 0.053 5046 Dihedral : 6.748 58.636 5231 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.81 % Allowed : 11.73 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.14), residues: 3555 helix: 1.56 (0.20), residues: 655 sheet: -0.50 (0.16), residues: 1028 loop : -0.91 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 314 TYR 0.024 0.001 TYR B 237 PHE 0.021 0.001 PHE C 39 TRP 0.007 0.001 TRP F 55 HIS 0.004 0.001 HIS C1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (29307) covalent geometry : angle 0.54941 / 0.28 (39824) SS BOND : bond 0.00235 / 0.16 ( 50) SS BOND : angle 1.39954 / 0.96 ( 100) hydrogen bonds : bond 0.03738 / 2.57 ( 1039) hydrogen bonds : angle 5.15004 / 3.66 ( 3165) link_ALPHA1-3 : bond 0.00597 / 0.30 ( 3) link_ALPHA1-3 : angle 1.55597 / 0.82 ( 9) link_ALPHA1-6 : bond 0.00846 / 0.44 ( 3) link_ALPHA1-6 : angle 1.54947 / 0.92 ( 9) link_BETA1-4 : bond 0.00282 / 0.18 ( 13) link_BETA1-4 : angle 2.04619 / 1.30 ( 39) link_NAG-ASN : bond 0.00454 / 0.33 ( 43) link_NAG-ASN : angle 2.46636 / 1.62 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 223 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8340 (ttm-80) cc_final: 0.7754 (ttp80) REVERT: A 270 HIS cc_start: 0.8638 (t70) cc_final: 0.8301 (m170) REVERT: A 824 THR cc_start: 0.8503 (p) cc_final: 0.8123 (p) REVERT: A 924 ARG cc_start: 0.8323 (mmp80) cc_final: 0.7847 (tpp80) REVERT: F 53 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.6493 (tp) REVERT: F 89 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6262 (tmt) REVERT: F 102 MET cc_start: 0.6766 (mmp) cc_final: 0.6026 (mmt) REVERT: B 490 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6575 (mpt-90) REVERT: B 543 CYS cc_start: 0.7148 (t) cc_final: 0.6921 (t) REVERT: B 924 ARG cc_start: 0.8244 (mtm-85) cc_final: 0.7984 (mtm110) REVERT: B 939 MET cc_start: 0.9106 (mtm) cc_final: 0.8712 (mtm) REVERT: B 979 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: B 1165 ASP cc_start: 0.8425 (m-30) cc_final: 0.8172 (m-30) REVERT: C 34 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.6239 (mtm110) REVERT: C 35 PHE cc_start: 0.7342 (t80) cc_final: 0.6586 (t80) REVERT: C 42 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.7284 (mp10) REVERT: C 228 GLN cc_start: 0.6649 (tt0) cc_final: 0.6132 (tm-30) REVERT: C 452 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: C 460 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7882 (ptm160) REVERT: C 592 THR cc_start: 0.8541 (m) cc_final: 0.8317 (p) REVERT: C 682 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7489 (mt0) REVERT: C 967 THR cc_start: 0.7140 (p) cc_final: 0.6698 (t) REVERT: C 996 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.6647 (tm-30) REVERT: C 1113 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8567 (mtpm) REVERT: C 1162 ASP cc_start: 0.7677 (m-30) cc_final: 0.7322 (t70) REVERT: C 1235 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6420 (ttm110) REVERT: C 1240 ASP cc_start: 0.7810 (t70) cc_final: 0.6889 (m-30) outliers start: 56 outliers final: 41 residues processed: 259 average time/residue: 0.5853 time to fit residues: 182.7711 Evaluate side-chains 272 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 979 GLN Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 460 ARG Chi-restraints excluded: chain C residue 491 ASN Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 682 GLN Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 817 SER Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 948 GLU Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1077 LEU Chi-restraints excluded: chain C residue 1113 LYS Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1235 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 234 optimal weight: 0.5980 chunk 330 optimal weight: 0.8980 chunk 270 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 202 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 301 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 HIS B 825 GLN C 270 HIS C 300 ASN C 571 ASN C1222 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.149813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112489 restraints weight = 38458.243| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.46 r_work: 0.3138 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29419 Z= 0.160 Angle : 0.571 10.217 40110 Z= 0.287 Chirality : 0.045 0.267 4726 Planarity : 0.004 0.051 5046 Dihedral : 6.740 58.184 5231 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.94 % Allowed : 11.76 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.14), residues: 3555 helix: 1.54 (0.20), residues: 655 sheet: -0.51 (0.16), residues: 1034 loop : -0.91 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 314 TYR 0.025 0.001 TYR B 237 PHE 0.021 0.001 PHE C 39 TRP 0.008 0.001 TRP F 55 HIS 0.007 0.001 HIS B 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (29307) covalent geometry : angle 0.54667 / 0.28 (39824) SS BOND : bond 0.00235 / 0.16 ( 50) SS BOND : angle 1.42852 / 0.97 ( 100) hydrogen bonds : bond 0.03703 / 2.54 ( 1039) hydrogen bonds : angle 5.14236 / 3.65 ( 3165) link_ALPHA1-3 : bond 0.00641 / 0.32 ( 3) link_ALPHA1-3 : angle 1.48874 / 0.79 ( 9) link_ALPHA1-6 : bond 0.00844 / 0.43 ( 3) link_ALPHA1-6 : angle 1.52175 / 0.91 ( 9) link_BETA1-4 : bond 0.00275 / 0.17 ( 13) link_BETA1-4 : angle 2.02549 / 1.29 ( 39) link_NAG-ASN : bond 0.00442 / 0.32 ( 43) link_NAG-ASN : angle 2.44968 / 1.61 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12267.46 seconds wall clock time: 209 minutes 28.32 seconds (12568.32 seconds total)