Starting phenix.real_space_refine on Fri Mar 6 02:05:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n1q_24121/03_2026/7n1q_24121.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n1q_24121/03_2026/7n1q_24121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n1q_24121/03_2026/7n1q_24121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n1q_24121/03_2026/7n1q_24121.map" model { file = "/net/cci-nas-00/data/ceres_data/7n1q_24121/03_2026/7n1q_24121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n1q_24121/03_2026/7n1q_24121.cif" } resolution = 2.9 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= 0.003 sd= 0.044 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 117 5.16 5 C 17169 2.51 5 N 4380 2.21 5 O 5346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27012 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 8598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8598 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 52, 'TRANS': 1045} Chain breaks: 5 Chain: "B" Number of atoms: 8475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8475 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 6 Chain: "C" Number of atoms: 8653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1104, 8653 Classifications: {'peptide': 1104} Link IDs: {'PTRANS': 53, 'TRANS': 1050} Chain breaks: 4 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: "F" 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: "G" 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "c" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.02, per 1000 atoms: 0.22 Number of scatterers: 27012 At special positions: 0 Unit cell: (149.337, 143.562, 216.168, 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 117 16.00 O 5346 8.00 N 4380 7.00 C 17169 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 Atom "HETATM26278 O5 NAG U 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM26758 O5 NAG A1411 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG S 2 " - " MAN S 3 " " NAG T 2 " - " MAN T 3 " " NAG d 2 " - " MAN d 3 " " NAG e 2 " - " MAN e 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG R 1 " - " FUC R 3 " " NAG c 1 " - " FUC c 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 149 " " NAG A1405 " - " ASN A 234 " " NAG A1406 " - " ASN A 282 " " NAG A1407 " - " ASN A 343 " " NAG A1408 " - " ASN A 603 " " NAG A1410 " - " ASN A 709 " " NAG A1411 " - " ASN A1158 " " NAG B1401 " - " ASN B 17 " " NAG B1402 " - " ASN B 61 " " NAG B1403 " - " ASN B 149 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 331 " " NAG B1406 " - " ASN B 343 " " NAG B1407 " - " ASN B 603 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B 709 " " NAG B1410 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 343 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 616 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 122 " " NAG M 1 " - " ASN B 165 " " NAG N 1 " - " ASN B 282 " " NAG O 1 " - " ASN B 616 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1074 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 17 " " NAG V 1 " - " ASN C 122 " " NAG W 1 " - " ASN C 165 " " NAG X 1 " - " ASN C 234 " " NAG Y 1 " - " ASN C 282 " " NAG Z 1 " - " ASN C 616 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 801 " " NAG c 1 " - " ASN C1074 " " NAG d 1 " - " ASN C1098 " " NAG e 1 " - " ASN C1134 " Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6146 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 50 sheets defined 27.9% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 6.209A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.149A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.534A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.537A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.975A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.780A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.327A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.767A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 848 removed outlier: 3.644A pdb=" N ALA A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 4.364A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.703A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.847A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.564A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.970A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 3.987A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.782A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.090A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.500A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.664A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.828A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.541A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.556A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.755A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.535A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.524A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.795A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.270A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1159 removed outlier: 3.913A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.799A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.689A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.901A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.504A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.035A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.630A pdb=" N ILE C 624 " --> pdb=" O PRO C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 639 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.772A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.960A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.389A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.502A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.708A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.863A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.554A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 1033 removed outlier: 4.373A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.095A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C1152 " --> pdb=" O PHE C1148 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.929A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.283A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.521A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.408A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.720A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.766A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.996A pdb=" N HIS A 245 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N SER A 247 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 141 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.854A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.243A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.606A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG A 246 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A 101 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.108A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.258A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.694A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.751A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.181A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.575A pdb=" N VAL A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LYS B 790 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.020A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.260A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.410A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.953A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.826A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 removed outlier: 7.002A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.475A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.649A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 13.456A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 13.348A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 13.655A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.944A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.942A pdb=" N HIS B 245 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N SER B 247 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU B 141 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.475A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.649A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.267A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.157A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.733A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.733A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.676A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.680A pdb=" N VAL B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LYS C 790 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.960A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.897A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.292A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.159A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.812A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.447A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.040A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.637A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.300A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.866A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N HIS C 245 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.637A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.840A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.510A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.510A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.256A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.507A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.216A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.258A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1094 through 1097 1154 hydrogen bonds defined for protein. 3144 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: 6.72 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 4316 1.30 - 1.43: 7429 1.43 - 1.56: 15719 1.56 - 1.69: 1 1.69 - 1.82: 147 Bond restraints: 27612 Sorted by residual: bond pdb=" CA ARG C1014 " pdb=" C ARG C1014 " ideal model delta sigma weight residual 1.524 1.438 0.085 1.29e-02 6.01e+03 4.36e+01 bond pdb=" C ARG C1014 " pdb=" O ARG C1014 " ideal model delta sigma weight residual 1.237 1.163 0.073 1.19e-02 7.06e+03 3.78e+01 bond pdb=" C ARG A 905 " pdb=" O ARG A 905 " ideal model delta sigma weight residual 1.237 1.169 0.067 1.19e-02 7.06e+03 3.19e+01 bond pdb=" C ARG C 237 " pdb=" O ARG C 237 " ideal model delta sigma weight residual 1.234 1.164 0.069 1.24e-02 6.50e+03 3.10e+01 bond pdb=" C ARG A1000 " pdb=" O ARG A1000 " ideal model delta sigma weight residual 1.236 1.173 0.063 1.22e-02 6.72e+03 2.66e+01 ... (remaining 27607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 31985 2.57 - 5.15: 5271 5.15 - 7.72: 280 7.72 - 10.30: 13 10.30 - 12.87: 1 Bond angle restraints: 37550 Sorted by residual: angle pdb=" OD1 ASN A 17 " pdb=" CG ASN A 17 " pdb=" ND2 ASN A 17 " ideal model delta sigma weight residual 122.60 114.72 7.88 1.00e+00 1.00e+00 6.22e+01 angle pdb=" CA HIS C 519 " pdb=" CB HIS C 519 " pdb=" CG HIS C 519 " ideal model delta sigma weight residual 113.80 121.37 -7.57 1.00e+00 1.00e+00 5.73e+01 angle pdb=" N ARG C1107 " pdb=" CA ARG C1107 " pdb=" C ARG C1107 " ideal model delta sigma weight residual 111.71 120.35 -8.64 1.15e+00 7.56e-01 5.65e+01 angle pdb=" N PRO B 25 " pdb=" CA PRO B 25 " pdb=" C PRO B 25 " ideal model delta sigma weight residual 110.70 119.41 -8.71 1.22e+00 6.72e-01 5.10e+01 angle pdb=" OE1 GLN C 935 " pdb=" CD GLN C 935 " pdb=" NE2 GLN C 935 " ideal model delta sigma weight residual 122.60 116.02 6.58 1.00e+00 1.00e+00 4.34e+01 ... (remaining 37545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.43: 16874 24.43 - 48.85: 598 48.85 - 73.28: 114 73.28 - 97.70: 39 97.70 - 122.13: 22 Dihedral angle restraints: 17647 sinusoidal: 8087 harmonic: 9560 Sorted by residual: dihedral pdb=" CA CYS B 617 " pdb=" C CYS B 617 " pdb=" N THR B 618 " pdb=" CA THR B 618 " ideal model delta harmonic sigma weight residual 180.00 150.05 29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA THR A 599 " pdb=" C THR A 599 " pdb=" N PRO A 600 " pdb=" CA PRO A 600 " ideal model delta harmonic sigma weight residual 180.00 150.48 29.52 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA SER B 494 " pdb=" C SER B 494 " pdb=" N TYR B 495 " pdb=" CA TYR B 495 " ideal model delta harmonic sigma weight residual 180.00 150.61 29.39 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 17644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.359: 4484 0.359 - 0.718: 19 0.718 - 1.076: 1 1.076 - 1.435: 0 1.435 - 1.794: 1 Chirality restraints: 4505 Sorted by residual: chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.40e+02 chirality pdb=" C1 MAN e 3 " pdb=" O4 NAG e 2 " pdb=" C2 MAN e 3 " pdb=" O5 MAN e 3 " both_signs ideal model delta sigma weight residual False 2.40 2.59 -0.19 2.00e-02 2.50e+03 8.97e+01 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.19e+01 ... (remaining 4502 not shown) Planarity restraints: 4783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.220 2.00e-02 2.50e+03 2.61e-01 8.52e+02 pdb=" CG ASN C 331 " -0.143 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.417 2.00e-02 2.50e+03 pdb=" C1 NAG C1403 " 0.311 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.143 2.00e-02 2.50e+03 1.52e-01 2.90e+02 pdb=" CG ASN B 234 " -0.085 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.237 2.00e-02 2.50e+03 pdb=" C1 NAG B1404 " 0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 17 " -0.079 2.00e-02 2.50e+03 1.21e-01 1.84e+02 pdb=" CG ASN C 17 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN C 17 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 17 " 0.207 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.151 2.00e-02 2.50e+03 ... (remaining 4780 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 39 2.53 - 3.12: 19459 3.12 - 3.72: 39891 3.72 - 4.31: 59210 4.31 - 4.90: 96623 Nonbonded interactions: 215222 Sorted by model distance: nonbonded pdb=" OH TYR B 91 " pdb=" OE2 GLU B 191 " model vdw 1.939 3.040 nonbonded pdb=" O ASN C 17 " pdb=" OD1 ASN C 17 " model vdw 1.941 3.040 nonbonded pdb=" NH2 ARG B 403 " pdb=" OE2 GLU B 406 " model vdw 1.944 3.120 nonbonded pdb=" ND2 ASN A 165 " pdb=" C1 NAG A1404 " model vdw 1.999 3.550 nonbonded pdb=" O MET C 900 " pdb=" CD2 TYR C 904 " model vdw 2.064 3.340 ... (remaining 215217 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 14 through 260 or resid 264 through 829 or resid 853 throu \ gh 1408)) selection = (chain 'B' and (resid 14 through 621 or resid 636 through 1408)) selection = (chain 'C' and (resid 14 through 178 or resid 182 through 260 or resid 264 throu \ gh 621 or resid 636 through 829 or resid 853 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 9.490 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: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.830 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.015 0.494 27747 Z= 0.815 Angle : 1.862 47.090 37912 Z= 1.189 Chirality : 0.109 1.794 4505 Planarity : 0.012 0.102 4728 Dihedral : 14.365 122.128 11372 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.13 % Favored : 93.22 % Rotamer: Outliers : 1.29 % Allowed : 3.80 % Favored : 94.91 % Cbeta Deviations : 0.33 % 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: -1.52 (0.13), residues: 3245 helix: -1.25 (0.16), residues: 728 sheet: 0.34 (0.20), residues: 609 loop : -1.39 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1107 TYR 0.115 0.020 TYR B 91 PHE 0.089 0.013 PHE C 718 TRP 0.129 0.028 TRP A 886 HIS 0.016 0.003 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.01406 (27612) covalent geometry : angle 1.78835 (37550) SS BOND : bond 0.01269 ( 43) SS BOND : angle 2.37879 ( 86) hydrogen bonds : bond 0.15520 ( 1120) hydrogen bonds : angle 8.52284 ( 3144) link_ALPHA1-4 : bond 0.02736 ( 6) link_ALPHA1-4 : angle 5.53324 ( 18) link_BETA1-4 : bond 0.02291 ( 28) link_BETA1-4 : angle 4.14465 ( 84) link_BETA1-6 : bond 0.03222 ( 3) link_BETA1-6 : angle 3.43416 ( 9) link_NAG-ASN : bond 0.09863 ( 55) link_NAG-ASN : angle 7.30146 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 685 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 132 GLU cc_start: 0.7644 (tp30) cc_final: 0.6824 (mm-30) REVERT: A 277 LEU cc_start: 0.8947 (mp) cc_final: 0.8746 (mm) REVERT: A 394 ASN cc_start: 0.8077 (p0) cc_final: 0.7536 (p0) REVERT: A 396 TYR cc_start: 0.6474 (m-80) cc_final: 0.5958 (m-80) REVERT: A 441 LEU cc_start: 0.7914 (mm) cc_final: 0.7712 (mm) REVERT: A 452 LEU cc_start: 0.7920 (mm) cc_final: 0.7264 (mm) REVERT: A 581 THR cc_start: 0.8673 (p) cc_final: 0.8026 (p) REVERT: A 583 GLU cc_start: 0.7578 (pm20) cc_final: 0.6914 (pm20) REVERT: A 737 ASP cc_start: 0.7844 (t0) cc_final: 0.7169 (t70) REVERT: A 740 MET cc_start: 0.7791 (ttm) cc_final: 0.7585 (ttm) REVERT: A 773 GLU cc_start: 0.7673 (tt0) cc_final: 0.7445 (tt0) REVERT: A 790 LYS cc_start: 0.8326 (mtpt) cc_final: 0.8051 (mmmm) REVERT: A 814 LYS cc_start: 0.8449 (mmpt) cc_final: 0.8241 (mmpt) REVERT: A 985 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7105 (p0) REVERT: A 986 LYS cc_start: 0.8634 (tptm) cc_final: 0.8388 (tppt) REVERT: A 988 GLU cc_start: 0.7687 (mp0) cc_final: 0.7231 (mp0) REVERT: A 994 ASP cc_start: 0.7786 (t70) cc_final: 0.7513 (t0) REVERT: A 1038 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8713 (mmmt) REVERT: A 1091 ARG cc_start: 0.8028 (mtt-85) cc_final: 0.7679 (mtt-85) REVERT: B 137 ASN cc_start: 0.8954 (t0) cc_final: 0.8547 (t0) REVERT: B 207 HIS cc_start: 0.6767 (m-70) cc_final: 0.6039 (m170) REVERT: B 319 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8404 (ttm-80) REVERT: B 405 ASP cc_start: 0.7472 (p0) cc_final: 0.7212 (p0) REVERT: B 421 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.6590 (p90) REVERT: B 571 ASP cc_start: 0.7804 (t70) cc_final: 0.7512 (t0) REVERT: B 825 LYS cc_start: 0.8736 (mmmm) cc_final: 0.8465 (mttm) REVERT: B 856 ASN cc_start: 0.7417 (m110) cc_final: 0.7165 (m-40) REVERT: B 994 ASP cc_start: 0.7989 (t70) cc_final: 0.7739 (t0) REVERT: B 1050 MET cc_start: 0.8632 (ptm) cc_final: 0.8415 (ptm) REVERT: B 1084 ASP cc_start: 0.7641 (p0) cc_final: 0.7325 (p0) REVERT: B 1107 ARG cc_start: 0.7686 (mtt-85) cc_final: 0.7474 (mtt180) REVERT: B 1118 ASP cc_start: 0.7757 (t70) cc_final: 0.7535 (t0) REVERT: B 1119 ASN cc_start: 0.8024 (m-40) cc_final: 0.7794 (m110) REVERT: C 121 ASN cc_start: 0.7783 (t0) cc_final: 0.7471 (t0) REVERT: C 138 ASP cc_start: 0.7953 (m-30) cc_final: 0.7753 (m-30) REVERT: C 177 MET cc_start: 0.6787 (ptm) cc_final: 0.6495 (ptm) REVERT: C 187 LYS cc_start: 0.8870 (mtmm) cc_final: 0.8343 (mttp) REVERT: C 212 LEU cc_start: 0.8748 (mt) cc_final: 0.8531 (mt) REVERT: C 298 GLU cc_start: 0.7742 (tt0) cc_final: 0.7490 (tt0) REVERT: C 316 SER cc_start: 0.8975 (t) cc_final: 0.8568 (p) REVERT: C 319 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8126 (ptp-110) REVERT: C 329 PHE cc_start: 0.8766 (m-10) cc_final: 0.8474 (m-80) REVERT: C 574 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7668 (p0) REVERT: C 586 ASP cc_start: 0.7975 (m-30) cc_final: 0.7712 (m-30) REVERT: C 704 SER cc_start: 0.8722 (t) cc_final: 0.8479 (m) REVERT: C 790 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8305 (ptpp) REVERT: C 796 ASP cc_start: 0.7489 (t0) cc_final: 0.7182 (t0) REVERT: C 823 PHE cc_start: 0.7933 (m-80) cc_final: 0.7577 (m-80) REVERT: C 867 ASP cc_start: 0.8029 (m-30) cc_final: 0.7749 (m-30) REVERT: C 954 GLN cc_start: 0.8087 (mt0) cc_final: 0.7757 (mt0) REVERT: C 1017 GLU cc_start: 0.7855 (tt0) cc_final: 0.7626 (tt0) outliers start: 37 outliers final: 7 residues processed: 702 average time/residue: 0.6284 time to fit residues: 511.8318 Evaluate side-chains 531 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 518 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 995 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN A 99 ASN A 165 ASN A 271 GLN A 317 ASN A 907 ASN A 955 ASN A 957 GLN A1119 ASN B 52 GLN B 121 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 641 ASN B 644 GLN B 751 ASN B 779 GLN B 913 GLN B 955 ASN B1101 HIS C 14 GLN C 115 GLN C 125 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 460 ASN C 613 GLN C 644 GLN C 675 GLN C 935 GLN C 960 ASN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.108476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.087414 restraints weight = 57804.236| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.13 r_work: 0.3196 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 27747 Z= 0.173 Angle : 0.821 14.972 37912 Z= 0.402 Chirality : 0.049 0.371 4505 Planarity : 0.004 0.062 4728 Dihedral : 10.359 112.438 5518 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.79 % Favored : 95.96 % Rotamer: Outliers : 2.96 % Allowed : 12.59 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.48 (0.14), residues: 3245 helix: 0.85 (0.19), residues: 737 sheet: 0.31 (0.19), residues: 645 loop : -1.05 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 509 TYR 0.032 0.002 TYR B 904 PHE 0.023 0.002 PHE B1148 TRP 0.025 0.002 TRP A 152 HIS 0.006 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00390 (27612) covalent geometry : angle 0.77377 (37550) SS BOND : bond 0.00455 ( 43) SS BOND : angle 2.38450 ( 86) hydrogen bonds : bond 0.04666 ( 1120) hydrogen bonds : angle 6.30030 ( 3144) link_ALPHA1-4 : bond 0.01569 ( 6) link_ALPHA1-4 : angle 4.09273 ( 18) link_BETA1-4 : bond 0.00369 ( 28) link_BETA1-4 : angle 1.90654 ( 84) link_BETA1-6 : bond 0.01446 ( 3) link_BETA1-6 : angle 1.59028 ( 9) link_NAG-ASN : bond 0.00403 ( 55) link_NAG-ASN : angle 3.44643 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 539 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.7959 (p) cc_final: 0.7446 (p) REVERT: A 132 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: A 159 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8439 (t) REVERT: A 190 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7894 (mtt180) REVERT: A 319 ARG cc_start: 0.8594 (ttm110) cc_final: 0.8294 (ttm110) REVERT: A 326 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8342 (pp) REVERT: A 378 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8191 (ptmm) REVERT: A 441 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7761 (mm) REVERT: A 452 LEU cc_start: 0.7965 (mm) cc_final: 0.7057 (mm) REVERT: A 547 THR cc_start: 0.8997 (m) cc_final: 0.8779 (p) REVERT: A 581 THR cc_start: 0.8839 (p) cc_final: 0.8445 (p) REVERT: A 583 GLU cc_start: 0.7790 (pm20) cc_final: 0.7482 (pm20) REVERT: A 773 GLU cc_start: 0.8249 (tt0) cc_final: 0.7988 (tt0) REVERT: A 835 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8227 (mmtp) REVERT: A 985 ASP cc_start: 0.8379 (p0) cc_final: 0.7814 (p0) REVERT: A 988 GLU cc_start: 0.8472 (mp0) cc_final: 0.7897 (mp0) REVERT: A 994 ASP cc_start: 0.8495 (t70) cc_final: 0.8215 (t0) REVERT: A 995 ARG cc_start: 0.8771 (mtt-85) cc_final: 0.8513 (mtp180) REVERT: A 1126 CYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6945 (m) REVERT: B 52 GLN cc_start: 0.8251 (tp-100) cc_final: 0.8006 (tp-100) REVERT: B 137 ASN cc_start: 0.8778 (t0) cc_final: 0.8322 (t0) REVERT: B 177 MET cc_start: 0.5740 (mpp) cc_final: 0.4903 (ppp) REVERT: B 190 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7247 (mtt90) REVERT: B 216 LEU cc_start: 0.8189 (mt) cc_final: 0.7891 (mp) REVERT: B 319 ARG cc_start: 0.8861 (ttm110) cc_final: 0.8593 (ttm-80) REVERT: B 406 GLU cc_start: 0.7997 (tt0) cc_final: 0.7652 (tt0) REVERT: B 418 ILE cc_start: 0.8825 (mp) cc_final: 0.8393 (mp) REVERT: B 456 PHE cc_start: 0.8453 (m-80) cc_final: 0.8016 (m-80) REVERT: B 467 ASP cc_start: 0.7592 (p0) cc_final: 0.7357 (p0) REVERT: B 586 ASP cc_start: 0.8479 (m-30) cc_final: 0.8172 (m-30) REVERT: B 663 ASP cc_start: 0.8495 (t0) cc_final: 0.8247 (t0) REVERT: B 675 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7387 (mm-40) REVERT: B 725 GLU cc_start: 0.8511 (tt0) cc_final: 0.8285 (tt0) REVERT: B 856 ASN cc_start: 0.7857 (m110) cc_final: 0.7573 (m-40) REVERT: B 994 ASP cc_start: 0.8549 (t70) cc_final: 0.8259 (t0) REVERT: B 1045 LYS cc_start: 0.8737 (tppp) cc_final: 0.8433 (mmmt) REVERT: B 1118 ASP cc_start: 0.8660 (t70) cc_final: 0.8453 (t0) REVERT: B 1119 ASN cc_start: 0.8590 (m-40) cc_final: 0.8281 (m110) REVERT: C 81 ASN cc_start: 0.7821 (m-40) cc_final: 0.7540 (m-40) REVERT: C 121 ASN cc_start: 0.7861 (t0) cc_final: 0.7546 (t0) REVERT: C 138 ASP cc_start: 0.8515 (m-30) cc_final: 0.8245 (m-30) REVERT: C 153 MET cc_start: 0.5348 (mpt) cc_final: 0.5144 (mpt) REVERT: C 177 MET cc_start: 0.6870 (ptm) cc_final: 0.6502 (ptm) REVERT: C 187 LYS cc_start: 0.8825 (mtmm) cc_final: 0.8280 (ttpp) REVERT: C 237 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7723 (ptm-80) REVERT: C 269 TYR cc_start: 0.8687 (m-80) cc_final: 0.8421 (m-10) REVERT: C 281 GLU cc_start: 0.8817 (pt0) cc_final: 0.8466 (pm20) REVERT: C 316 SER cc_start: 0.9154 (t) cc_final: 0.8833 (p) REVERT: C 324 GLU cc_start: 0.8302 (pm20) cc_final: 0.7922 (pm20) REVERT: C 357 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8170 (ttm-80) REVERT: C 437 ASN cc_start: 0.7955 (t0) cc_final: 0.7537 (t0) REVERT: C 574 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8136 (p0) REVERT: C 586 ASP cc_start: 0.8368 (m-30) cc_final: 0.8078 (m-30) REVERT: C 602 THR cc_start: 0.9090 (m) cc_final: 0.8743 (p) REVERT: C 634 ARG cc_start: 0.7679 (tpp80) cc_final: 0.7271 (mmt90) REVERT: C 737 ASP cc_start: 0.7879 (t0) cc_final: 0.7628 (t0) REVERT: C 776 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8272 (tttp) REVERT: C 780 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8217 (mm-30) REVERT: C 796 ASP cc_start: 0.8007 (t0) cc_final: 0.7583 (t0) REVERT: C 867 ASP cc_start: 0.8405 (m-30) cc_final: 0.8201 (m-30) REVERT: C 950 ASP cc_start: 0.8559 (t0) cc_final: 0.8115 (t0) REVERT: C 954 GLN cc_start: 0.8503 (mt0) cc_final: 0.8195 (mt0) REVERT: C 957 GLN cc_start: 0.8486 (tp40) cc_final: 0.8240 (tt0) REVERT: C 988 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7829 (mm-30) REVERT: C 1017 GLU cc_start: 0.8693 (tt0) cc_final: 0.8454 (tt0) REVERT: C 1148 PHE cc_start: 0.7585 (t80) cc_final: 0.7371 (t80) outliers start: 85 outliers final: 27 residues processed: 582 average time/residue: 0.5932 time to fit residues: 405.1542 Evaluate side-chains 511 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 471 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 776 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 214 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 191 optimal weight: 0.7980 chunk 217 optimal weight: 0.0970 chunk 142 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 324 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 270 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 196 ASN A 394 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 957 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 955 ASN B1101 HIS C 188 ASN C 207 HIS C 245 HIS C 354 ASN C 388 ASN C 644 GLN C 675 GLN C 856 ASN C1002 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.107947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.086907 restraints weight = 57787.952| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.14 r_work: 0.3192 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27747 Z= 0.157 Angle : 0.754 18.300 37912 Z= 0.363 Chirality : 0.046 0.320 4505 Planarity : 0.004 0.062 4728 Dihedral : 9.618 109.687 5481 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.47 % Favored : 95.35 % Rotamer: Outliers : 3.28 % Allowed : 14.44 % Favored : 82.29 % 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: -0.31 (0.14), residues: 3245 helix: 1.43 (0.19), residues: 748 sheet: -0.03 (0.18), residues: 707 loop : -1.01 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 646 TYR 0.023 0.002 TYR C 453 PHE 0.026 0.002 PHE A 392 TRP 0.030 0.002 TRP A 152 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00360 (27612) covalent geometry : angle 0.70381 (37550) SS BOND : bond 0.00540 ( 43) SS BOND : angle 1.94866 ( 86) hydrogen bonds : bond 0.04147 ( 1120) hydrogen bonds : angle 5.93000 ( 3144) link_ALPHA1-4 : bond 0.01688 ( 6) link_ALPHA1-4 : angle 4.05049 ( 18) link_BETA1-4 : bond 0.00298 ( 28) link_BETA1-4 : angle 1.63561 ( 84) link_BETA1-6 : bond 0.01389 ( 3) link_BETA1-6 : angle 1.80971 ( 9) link_NAG-ASN : bond 0.00354 ( 55) link_NAG-ASN : angle 3.56111 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 490 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.7908 (p) cc_final: 0.7439 (p) REVERT: A 132 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7052 (mm-30) REVERT: A 159 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8456 (t) REVERT: A 190 ARG cc_start: 0.8091 (ttm170) cc_final: 0.7762 (ttt180) REVERT: A 245 HIS cc_start: 0.6807 (m-70) cc_final: 0.6408 (m90) REVERT: A 319 ARG cc_start: 0.8603 (ttm110) cc_final: 0.8321 (ttm110) REVERT: A 357 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7706 (ttm-80) REVERT: A 394 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7919 (p0) REVERT: A 396 TYR cc_start: 0.6691 (m-80) cc_final: 0.6315 (m-80) REVERT: A 441 LEU cc_start: 0.7892 (mm) cc_final: 0.7584 (mm) REVERT: A 448 ASN cc_start: 0.5631 (m-40) cc_final: 0.4377 (m-40) REVERT: A 451 TYR cc_start: 0.7802 (m-80) cc_final: 0.7288 (m-80) REVERT: A 452 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7550 (mm) REVERT: A 547 THR cc_start: 0.8928 (m) cc_final: 0.8674 (p) REVERT: A 560 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8872 (mp) REVERT: A 581 THR cc_start: 0.8815 (p) cc_final: 0.8498 (p) REVERT: A 583 GLU cc_start: 0.7689 (pm20) cc_final: 0.7389 (pm20) REVERT: A 790 LYS cc_start: 0.8850 (mmmm) cc_final: 0.8606 (mtmt) REVERT: A 950 ASP cc_start: 0.8410 (m-30) cc_final: 0.8126 (m-30) REVERT: A 988 GLU cc_start: 0.8403 (mp0) cc_final: 0.7826 (mp0) REVERT: A 994 ASP cc_start: 0.8452 (t70) cc_final: 0.8145 (t0) REVERT: A 995 ARG cc_start: 0.8699 (mtt-85) cc_final: 0.8475 (mtp180) REVERT: B 137 ASN cc_start: 0.8754 (t0) cc_final: 0.8287 (t0) REVERT: B 207 HIS cc_start: 0.6563 (m170) cc_final: 0.6167 (m170) REVERT: B 278 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8644 (ttpt) REVERT: B 319 ARG cc_start: 0.8867 (ttm110) cc_final: 0.8630 (ttm-80) REVERT: B 406 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: B 467 ASP cc_start: 0.7498 (p0) cc_final: 0.7245 (p0) REVERT: B 586 ASP cc_start: 0.8452 (m-30) cc_final: 0.8156 (m-30) REVERT: B 725 GLU cc_start: 0.8509 (tt0) cc_final: 0.8290 (tt0) REVERT: B 859 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8779 (p) REVERT: B 994 ASP cc_start: 0.8520 (t70) cc_final: 0.8232 (t0) REVERT: B 1084 ASP cc_start: 0.8584 (p0) cc_final: 0.8366 (p0) REVERT: B 1118 ASP cc_start: 0.8667 (t70) cc_final: 0.8458 (t0) REVERT: B 1119 ASN cc_start: 0.8609 (m-40) cc_final: 0.8287 (m110) REVERT: C 121 ASN cc_start: 0.7764 (t0) cc_final: 0.7504 (t0) REVERT: C 138 ASP cc_start: 0.8451 (m-30) cc_final: 0.8169 (m-30) REVERT: C 187 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8333 (ttmt) REVERT: C 188 ASN cc_start: 0.8558 (t0) cc_final: 0.8332 (t0) REVERT: C 190 ARG cc_start: 0.8818 (ttm110) cc_final: 0.8532 (ttm-80) REVERT: C 237 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7861 (ptm-80) REVERT: C 281 GLU cc_start: 0.8821 (pt0) cc_final: 0.8448 (pm20) REVERT: C 316 SER cc_start: 0.9113 (t) cc_final: 0.8816 (p) REVERT: C 357 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8160 (ttm-80) REVERT: C 465 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7834 (tm-30) REVERT: C 586 ASP cc_start: 0.8327 (m-30) cc_final: 0.8075 (m-30) REVERT: C 602 THR cc_start: 0.9076 (m) cc_final: 0.8756 (p) REVERT: C 634 ARG cc_start: 0.7615 (tpp80) cc_final: 0.7141 (mmt90) REVERT: C 776 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8315 (tttp) REVERT: C 780 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8266 (mm-30) REVERT: C 796 ASP cc_start: 0.8100 (t0) cc_final: 0.7681 (t0) REVERT: C 950 ASP cc_start: 0.8562 (t0) cc_final: 0.8195 (t0) REVERT: C 957 GLN cc_start: 0.8489 (tp40) cc_final: 0.8245 (tt0) REVERT: C 988 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7756 (mm-30) REVERT: C 994 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8195 (t0) REVERT: C 1017 GLU cc_start: 0.8658 (tt0) cc_final: 0.8364 (tt0) outliers start: 94 outliers final: 30 residues processed: 544 average time/residue: 0.6161 time to fit residues: 392.7631 Evaluate side-chains 500 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 460 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 273 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 310 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 252 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 196 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 755 GLN C 207 HIS C 245 HIS C 317 ASN C 437 ASN C 460 ASN C 519 HIS C 644 GLN C 675 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.106396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.085149 restraints weight = 57854.405| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.16 r_work: 0.3160 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 27747 Z= 0.208 Angle : 0.758 13.433 37912 Z= 0.364 Chirality : 0.047 0.437 4505 Planarity : 0.004 0.068 4728 Dihedral : 9.212 106.833 5479 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.41 % Favored : 95.38 % Rotamer: Outliers : 3.91 % Allowed : 14.96 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.33 (0.14), residues: 3245 helix: 1.63 (0.19), residues: 742 sheet: -0.16 (0.18), residues: 690 loop : -1.04 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 214 TYR 0.023 0.002 TYR C 453 PHE 0.021 0.002 PHE C 490 TRP 0.028 0.002 TRP A 152 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00480 (27612) covalent geometry : angle 0.71320 (37550) SS BOND : bond 0.00467 ( 43) SS BOND : angle 2.08455 ( 86) hydrogen bonds : bond 0.04111 ( 1120) hydrogen bonds : angle 5.81132 ( 3144) link_ALPHA1-4 : bond 0.01746 ( 6) link_ALPHA1-4 : angle 4.27257 ( 18) link_BETA1-4 : bond 0.00238 ( 28) link_BETA1-4 : angle 1.58887 ( 84) link_BETA1-6 : bond 0.01395 ( 3) link_BETA1-6 : angle 2.10761 ( 9) link_NAG-ASN : bond 0.00369 ( 55) link_NAG-ASN : angle 3.24628 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 483 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.7945 (p) cc_final: 0.7495 (p) REVERT: A 132 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7129 (mm-30) REVERT: A 245 HIS cc_start: 0.6875 (m-70) cc_final: 0.6481 (m90) REVERT: A 319 ARG cc_start: 0.8670 (ttm110) cc_final: 0.8396 (ttm110) REVERT: A 380 TYR cc_start: 0.7017 (m-80) cc_final: 0.6347 (m-80) REVERT: A 395 VAL cc_start: 0.8234 (t) cc_final: 0.7933 (t) REVERT: A 441 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7602 (mm) REVERT: A 448 ASN cc_start: 0.6728 (m-40) cc_final: 0.6273 (m-40) REVERT: A 452 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7847 (mm) REVERT: A 790 LYS cc_start: 0.8821 (mmmm) cc_final: 0.8507 (mtmm) REVERT: A 808 ASP cc_start: 0.8332 (t0) cc_final: 0.7912 (t0) REVERT: A 918 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: A 950 ASP cc_start: 0.8486 (m-30) cc_final: 0.8186 (m-30) REVERT: A 988 GLU cc_start: 0.8357 (mp0) cc_final: 0.7779 (mp0) REVERT: A 994 ASP cc_start: 0.8453 (t70) cc_final: 0.8127 (t0) REVERT: A 995 ARG cc_start: 0.8760 (mtt-85) cc_final: 0.8523 (mtp180) REVERT: B 137 ASN cc_start: 0.8799 (t0) cc_final: 0.8517 (t0) REVERT: B 190 ARG cc_start: 0.7751 (mpt180) cc_final: 0.7431 (mtt90) REVERT: B 319 ARG cc_start: 0.8845 (ttm110) cc_final: 0.8602 (ttm-80) REVERT: B 408 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8146 (ptm-80) REVERT: B 467 ASP cc_start: 0.7577 (p0) cc_final: 0.7270 (p0) REVERT: B 553 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8749 (p) REVERT: B 586 ASP cc_start: 0.8409 (m-30) cc_final: 0.8101 (m-30) REVERT: B 675 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7305 (mm-40) REVERT: B 702 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: B 725 GLU cc_start: 0.8528 (tt0) cc_final: 0.8304 (tt0) REVERT: B 859 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8804 (p) REVERT: B 912 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8483 (p) REVERT: B 994 ASP cc_start: 0.8544 (t70) cc_final: 0.8253 (t0) REVERT: B 1072 GLU cc_start: 0.8751 (pm20) cc_final: 0.8314 (pm20) REVERT: B 1118 ASP cc_start: 0.8662 (t70) cc_final: 0.8455 (t0) REVERT: C 121 ASN cc_start: 0.7847 (t0) cc_final: 0.7582 (t0) REVERT: C 138 ASP cc_start: 0.8460 (m-30) cc_final: 0.8163 (m-30) REVERT: C 187 LYS cc_start: 0.8812 (mtmm) cc_final: 0.8524 (mtpp) REVERT: C 188 ASN cc_start: 0.8498 (t0) cc_final: 0.8291 (t0) REVERT: C 190 ARG cc_start: 0.8862 (ttm110) cc_final: 0.8513 (ttm-80) REVERT: C 237 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7842 (ptm-80) REVERT: C 465 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7941 (tm-30) REVERT: C 586 ASP cc_start: 0.8306 (m-30) cc_final: 0.8080 (m-30) REVERT: C 602 THR cc_start: 0.9105 (m) cc_final: 0.8793 (p) REVERT: C 634 ARG cc_start: 0.7648 (tpp80) cc_final: 0.7196 (mmt90) REVERT: C 780 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8276 (mm-30) REVERT: C 796 ASP cc_start: 0.8137 (t0) cc_final: 0.7730 (t0) REVERT: C 950 ASP cc_start: 0.8590 (t0) cc_final: 0.7990 (t0) REVERT: C 954 GLN cc_start: 0.8679 (mt0) cc_final: 0.8337 (mt0) REVERT: C 957 GLN cc_start: 0.8498 (tp40) cc_final: 0.8289 (tt0) REVERT: C 988 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7794 (mm-30) REVERT: C 1148 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6251 (t80) outliers start: 112 outliers final: 39 residues processed: 542 average time/residue: 0.6097 time to fit residues: 387.7226 Evaluate side-chains 504 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 454 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 45 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 137 ASN A 196 ASN A 487 ASN A 804 GLN A 935 GLN A 957 GLN A1010 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS B1101 HIS B1119 ASN C 134 GLN C 317 ASN C 437 ASN C 613 GLN C 644 GLN C 675 GLN C 804 GLN C 856 ASN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.105498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.084408 restraints weight = 58030.867| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.15 r_work: 0.3149 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 27747 Z= 0.235 Angle : 0.766 12.212 37912 Z= 0.371 Chirality : 0.047 0.329 4505 Planarity : 0.004 0.062 4728 Dihedral : 8.987 103.954 5479 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.75 % Favored : 95.10 % Rotamer: Outliers : 3.77 % Allowed : 16.70 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3245 helix: 1.54 (0.19), residues: 755 sheet: -0.14 (0.18), residues: 682 loop : -1.12 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 214 TYR 0.025 0.002 TYR C 904 PHE 0.019 0.002 PHE C 456 TRP 0.027 0.002 TRP A 152 HIS 0.013 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00545 (27612) covalent geometry : angle 0.72801 (37550) SS BOND : bond 0.00503 ( 43) SS BOND : angle 2.27391 ( 86) hydrogen bonds : bond 0.04136 ( 1120) hydrogen bonds : angle 5.77192 ( 3144) link_ALPHA1-4 : bond 0.01659 ( 6) link_ALPHA1-4 : angle 4.49120 ( 18) link_BETA1-4 : bond 0.00216 ( 28) link_BETA1-4 : angle 1.57351 ( 84) link_BETA1-6 : bond 0.01567 ( 3) link_BETA1-6 : angle 2.21898 ( 9) link_NAG-ASN : bond 0.00396 ( 55) link_NAG-ASN : angle 2.81820 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 468 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.7997 (p) cc_final: 0.7551 (p) REVERT: A 129 LYS cc_start: 0.8003 (ttmt) cc_final: 0.7790 (ttmp) REVERT: A 132 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6932 (mm-30) REVERT: A 173 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: A 190 ARG cc_start: 0.8289 (ttm170) cc_final: 0.8074 (mtt180) REVERT: A 245 HIS cc_start: 0.6929 (m-70) cc_final: 0.6631 (m90) REVERT: A 319 ARG cc_start: 0.8663 (ttm110) cc_final: 0.8378 (ttm110) REVERT: A 395 VAL cc_start: 0.8320 (t) cc_final: 0.7695 (t) REVERT: A 396 TYR cc_start: 0.7211 (m-80) cc_final: 0.6259 (m-80) REVERT: A 441 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7715 (mm) REVERT: A 442 ASP cc_start: 0.5376 (t0) cc_final: 0.5099 (t0) REVERT: A 448 ASN cc_start: 0.6678 (m-40) cc_final: 0.6319 (m110) REVERT: A 586 ASP cc_start: 0.8214 (m-30) cc_final: 0.7887 (m-30) REVERT: A 790 LYS cc_start: 0.8786 (mmmm) cc_final: 0.8554 (mtmm) REVERT: A 808 ASP cc_start: 0.8309 (t0) cc_final: 0.7883 (t0) REVERT: A 918 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: A 950 ASP cc_start: 0.8501 (m-30) cc_final: 0.8187 (m-30) REVERT: A 988 GLU cc_start: 0.8371 (mp0) cc_final: 0.7771 (mp0) REVERT: A 994 ASP cc_start: 0.8500 (t70) cc_final: 0.8182 (t0) REVERT: A 995 ARG cc_start: 0.8757 (mtt-85) cc_final: 0.8513 (mtp180) REVERT: B 137 ASN cc_start: 0.8963 (t0) cc_final: 0.8479 (t0) REVERT: B 319 ARG cc_start: 0.8861 (ttm110) cc_final: 0.8621 (ttm-80) REVERT: B 408 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8149 (ptm-80) REVERT: B 467 ASP cc_start: 0.7616 (p0) cc_final: 0.7294 (p0) REVERT: B 586 ASP cc_start: 0.8422 (m-30) cc_final: 0.8173 (m-30) REVERT: B 646 ARG cc_start: 0.8839 (mtm-85) cc_final: 0.8558 (mtm110) REVERT: B 663 ASP cc_start: 0.8651 (t0) cc_final: 0.8436 (t0) REVERT: B 702 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: B 725 GLU cc_start: 0.8555 (tt0) cc_final: 0.8315 (tt0) REVERT: B 855 PHE cc_start: 0.6660 (OUTLIER) cc_final: 0.6382 (p90) REVERT: B 859 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8801 (p) REVERT: B 994 ASP cc_start: 0.8472 (t70) cc_final: 0.8212 (t0) REVERT: B 1072 GLU cc_start: 0.8768 (pm20) cc_final: 0.8320 (pm20) REVERT: B 1107 ARG cc_start: 0.8341 (mtt180) cc_final: 0.8129 (mtt-85) REVERT: B 1118 ASP cc_start: 0.8641 (t70) cc_final: 0.8417 (t0) REVERT: C 121 ASN cc_start: 0.7902 (t0) cc_final: 0.7608 (t0) REVERT: C 138 ASP cc_start: 0.8448 (m-30) cc_final: 0.8168 (m-30) REVERT: C 187 LYS cc_start: 0.8826 (mtmm) cc_final: 0.8439 (ttpt) REVERT: C 237 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7898 (ptm-80) REVERT: C 269 TYR cc_start: 0.8613 (m-10) cc_final: 0.8252 (m-80) REVERT: C 382 VAL cc_start: 0.9354 (OUTLIER) cc_final: 0.9145 (t) REVERT: C 586 ASP cc_start: 0.8314 (m-30) cc_final: 0.8060 (m-30) REVERT: C 602 THR cc_start: 0.9108 (m) cc_final: 0.8816 (p) REVERT: C 634 ARG cc_start: 0.7693 (tpp80) cc_final: 0.7241 (mmt90) REVERT: C 780 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8278 (mm-30) REVERT: C 790 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8677 (ptpp) REVERT: C 796 ASP cc_start: 0.8158 (t0) cc_final: 0.7751 (t0) REVERT: C 935 GLN cc_start: 0.8545 (tt0) cc_final: 0.8213 (tt0) REVERT: C 950 ASP cc_start: 0.8587 (t0) cc_final: 0.7904 (t0) REVERT: C 954 GLN cc_start: 0.8658 (mt0) cc_final: 0.8255 (mt0) REVERT: C 988 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7833 (mm-30) REVERT: C 1148 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6403 (t80) outliers start: 108 outliers final: 49 residues processed: 530 average time/residue: 0.5816 time to fit residues: 362.2907 Evaluate side-chains 501 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 440 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 284 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 231 optimal weight: 0.3980 chunk 245 optimal weight: 0.7980 chunk 281 optimal weight: 0.7980 chunk 239 optimal weight: 1.9990 chunk 314 optimal weight: 0.6980 chunk 236 optimal weight: 3.9990 chunk 276 optimal weight: 0.8980 chunk 242 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 137 ASN A 196 ASN A 239 GLN A 394 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 394 ASN B 755 GLN B1101 HIS C 188 ASN C 207 HIS C 437 ASN C 460 ASN C 644 GLN C 675 GLN C 856 ASN C1002 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.106814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.085787 restraints weight = 57379.381| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.12 r_work: 0.3175 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27747 Z= 0.159 Angle : 0.734 12.888 37912 Z= 0.354 Chirality : 0.046 0.308 4505 Planarity : 0.004 0.070 4728 Dihedral : 8.523 100.943 5479 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.59 % Favored : 95.29 % Rotamer: Outliers : 3.63 % Allowed : 17.54 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3245 helix: 1.80 (0.20), residues: 741 sheet: -0.20 (0.18), residues: 675 loop : -1.03 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 214 TYR 0.028 0.001 TYR A 369 PHE 0.015 0.001 PHE B 855 TRP 0.026 0.001 TRP A 436 HIS 0.012 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00364 (27612) covalent geometry : angle 0.69903 (37550) SS BOND : bond 0.00442 ( 43) SS BOND : angle 1.92515 ( 86) hydrogen bonds : bond 0.03829 ( 1120) hydrogen bonds : angle 5.65751 ( 3144) link_ALPHA1-4 : bond 0.01628 ( 6) link_ALPHA1-4 : angle 4.26380 ( 18) link_BETA1-4 : bond 0.00268 ( 28) link_BETA1-4 : angle 1.42252 ( 84) link_BETA1-6 : bond 0.01741 ( 3) link_BETA1-6 : angle 2.17069 ( 9) link_NAG-ASN : bond 0.00325 ( 55) link_NAG-ASN : angle 2.70186 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 481 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7907 (mmt-90) REVERT: A 132 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6918 (mm-30) REVERT: A 319 ARG cc_start: 0.8655 (ttm110) cc_final: 0.8402 (ttm110) REVERT: A 392 PHE cc_start: 0.7839 (m-80) cc_final: 0.7596 (m-10) REVERT: A 394 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7751 (p0) REVERT: A 395 VAL cc_start: 0.8331 (t) cc_final: 0.7873 (t) REVERT: A 442 ASP cc_start: 0.5436 (t0) cc_final: 0.5176 (t0) REVERT: A 448 ASN cc_start: 0.6475 (m-40) cc_final: 0.5845 (m110) REVERT: A 586 ASP cc_start: 0.8206 (m-30) cc_final: 0.7856 (m-30) REVERT: A 790 LYS cc_start: 0.8758 (mmmm) cc_final: 0.8537 (mtmm) REVERT: A 808 ASP cc_start: 0.8315 (t0) cc_final: 0.7896 (t0) REVERT: A 918 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: A 950 ASP cc_start: 0.8470 (m-30) cc_final: 0.8161 (m-30) REVERT: A 988 GLU cc_start: 0.8347 (mp0) cc_final: 0.7755 (mp0) REVERT: A 994 ASP cc_start: 0.8470 (t70) cc_final: 0.8262 (t0) REVERT: A 995 ARG cc_start: 0.8719 (mtt-85) cc_final: 0.8428 (mtp180) REVERT: A 1045 LYS cc_start: 0.8883 (ttmm) cc_final: 0.8669 (tppp) REVERT: B 41 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8410 (mtmt) REVERT: B 137 ASN cc_start: 0.8893 (t0) cc_final: 0.8405 (t0) REVERT: B 319 ARG cc_start: 0.8840 (ttm110) cc_final: 0.8618 (ttm-80) REVERT: B 467 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7249 (p0) REVERT: B 553 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8790 (p) REVERT: B 586 ASP cc_start: 0.8401 (m-30) cc_final: 0.8144 (m-30) REVERT: B 646 ARG cc_start: 0.8821 (mtm-85) cc_final: 0.8537 (mtm110) REVERT: B 675 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7220 (mt0) REVERT: B 725 GLU cc_start: 0.8532 (tt0) cc_final: 0.8301 (tt0) REVERT: B 855 PHE cc_start: 0.6622 (OUTLIER) cc_final: 0.6378 (p90) REVERT: B 859 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8833 (p) REVERT: B 912 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8473 (p) REVERT: B 994 ASP cc_start: 0.8502 (t70) cc_final: 0.8207 (t0) REVERT: B 1072 GLU cc_start: 0.8703 (pm20) cc_final: 0.8266 (pm20) REVERT: B 1118 ASP cc_start: 0.8603 (t70) cc_final: 0.8392 (t0) REVERT: C 121 ASN cc_start: 0.7834 (t0) cc_final: 0.7579 (t0) REVERT: C 138 ASP cc_start: 0.8433 (m-30) cc_final: 0.8149 (m-30) REVERT: C 187 LYS cc_start: 0.8820 (mtmm) cc_final: 0.8469 (ttpt) REVERT: C 190 ARG cc_start: 0.8892 (ttp-110) cc_final: 0.8575 (ttm-80) REVERT: C 269 TYR cc_start: 0.8581 (m-10) cc_final: 0.8245 (m-80) REVERT: C 586 ASP cc_start: 0.8301 (m-30) cc_final: 0.8053 (m-30) REVERT: C 602 THR cc_start: 0.9102 (m) cc_final: 0.8836 (p) REVERT: C 634 ARG cc_start: 0.7684 (tpp80) cc_final: 0.7248 (mmt90) REVERT: C 780 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8155 (mm-30) REVERT: C 796 ASP cc_start: 0.8139 (t0) cc_final: 0.7747 (t0) REVERT: C 814 LYS cc_start: 0.8570 (mptt) cc_final: 0.8320 (mmpt) REVERT: C 912 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8484 (p) REVERT: C 933 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8533 (mttp) REVERT: C 935 GLN cc_start: 0.8452 (tt0) cc_final: 0.8238 (tt0) REVERT: C 950 ASP cc_start: 0.8573 (t0) cc_final: 0.7887 (t0) REVERT: C 954 GLN cc_start: 0.8668 (mt0) cc_final: 0.8253 (mt0) REVERT: C 988 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7776 (mm-30) REVERT: C 1148 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6658 (t80) outliers start: 104 outliers final: 46 residues processed: 537 average time/residue: 0.5585 time to fit residues: 354.5800 Evaluate side-chains 502 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 444 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 304 optimal weight: 0.7980 chunk 247 optimal weight: 0.5980 chunk 238 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 237 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 165 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 137 ASN A 196 ASN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 394 ASN B1101 HIS C 188 ASN C 317 ASN C 437 ASN C 644 GLN C 675 GLN C 969 ASN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.106904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.085913 restraints weight = 57270.025| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.12 r_work: 0.3179 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27747 Z= 0.163 Angle : 0.749 13.024 37912 Z= 0.361 Chirality : 0.046 0.309 4505 Planarity : 0.004 0.058 4728 Dihedral : 8.272 99.569 5475 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.75 % Favored : 95.13 % Rotamer: Outliers : 3.70 % Allowed : 18.48 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.26 (0.14), residues: 3245 helix: 1.83 (0.20), residues: 743 sheet: -0.20 (0.18), residues: 688 loop : -1.03 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 214 TYR 0.026 0.001 TYR B 453 PHE 0.020 0.001 PHE A 140 TRP 0.029 0.001 TRP A 436 HIS 0.015 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00375 (27612) covalent geometry : angle 0.71396 (37550) SS BOND : bond 0.00467 ( 43) SS BOND : angle 2.23052 ( 86) hydrogen bonds : bond 0.03792 ( 1120) hydrogen bonds : angle 5.60985 ( 3144) link_ALPHA1-4 : bond 0.01636 ( 6) link_ALPHA1-4 : angle 4.36645 ( 18) link_BETA1-4 : bond 0.00280 ( 28) link_BETA1-4 : angle 1.40400 ( 84) link_BETA1-6 : bond 0.01760 ( 3) link_BETA1-6 : angle 2.17670 ( 9) link_NAG-ASN : bond 0.00368 ( 55) link_NAG-ASN : angle 2.64054 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 460 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8259 (mmm160) cc_final: 0.7891 (mmt-90) REVERT: A 115 GLN cc_start: 0.8155 (mp10) cc_final: 0.7789 (mp10) REVERT: A 116 SER cc_start: 0.8674 (m) cc_final: 0.8001 (p) REVERT: A 132 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6871 (mm-30) REVERT: A 190 ARG cc_start: 0.8058 (ttm170) cc_final: 0.7751 (mtt180) REVERT: A 319 ARG cc_start: 0.8688 (ttm110) cc_final: 0.8436 (ttm110) REVERT: A 394 ASN cc_start: 0.7914 (p0) cc_final: 0.7611 (p0) REVERT: A 395 VAL cc_start: 0.8276 (t) cc_final: 0.7766 (t) REVERT: A 448 ASN cc_start: 0.6395 (m-40) cc_final: 0.6077 (m110) REVERT: A 586 ASP cc_start: 0.8225 (m-30) cc_final: 0.7852 (m-30) REVERT: A 790 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8526 (mtmm) REVERT: A 808 ASP cc_start: 0.8306 (t0) cc_final: 0.7900 (t0) REVERT: A 918 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: A 950 ASP cc_start: 0.8469 (m-30) cc_final: 0.8144 (m-30) REVERT: A 988 GLU cc_start: 0.8330 (mp0) cc_final: 0.7725 (mp0) REVERT: A 994 ASP cc_start: 0.8560 (t70) cc_final: 0.8256 (t0) REVERT: A 995 ARG cc_start: 0.8705 (mtt-85) cc_final: 0.8390 (mtp180) REVERT: A 1045 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8690 (tppp) REVERT: A 1146 ASP cc_start: 0.8123 (m-30) cc_final: 0.7873 (m-30) REVERT: B 41 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8418 (mtmt) REVERT: B 137 ASN cc_start: 0.8892 (t0) cc_final: 0.8400 (t0) REVERT: B 319 ARG cc_start: 0.8847 (ttm110) cc_final: 0.8635 (ttm-80) REVERT: B 408 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8078 (ptm-80) REVERT: B 467 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7287 (p0) REVERT: B 586 ASP cc_start: 0.8403 (m-30) cc_final: 0.8158 (m-30) REVERT: B 646 ARG cc_start: 0.8834 (mtm-85) cc_final: 0.8495 (mtm110) REVERT: B 675 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7234 (mt0) REVERT: B 725 GLU cc_start: 0.8536 (tt0) cc_final: 0.8318 (tt0) REVERT: B 855 PHE cc_start: 0.6624 (OUTLIER) cc_final: 0.6370 (p90) REVERT: B 912 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8474 (p) REVERT: B 994 ASP cc_start: 0.8463 (t70) cc_final: 0.8154 (t0) REVERT: B 1072 GLU cc_start: 0.8733 (pm20) cc_final: 0.8287 (pm20) REVERT: B 1118 ASP cc_start: 0.8584 (t70) cc_final: 0.8372 (t0) REVERT: C 121 ASN cc_start: 0.7824 (t0) cc_final: 0.7563 (t0) REVERT: C 138 ASP cc_start: 0.8439 (m-30) cc_final: 0.8152 (m-30) REVERT: C 187 LYS cc_start: 0.8802 (mtmm) cc_final: 0.8455 (ttpt) REVERT: C 269 TYR cc_start: 0.8569 (m-10) cc_final: 0.8232 (m-80) REVERT: C 574 ASP cc_start: 0.8136 (p0) cc_final: 0.7648 (t0) REVERT: C 586 ASP cc_start: 0.8284 (m-30) cc_final: 0.8050 (m-30) REVERT: C 602 THR cc_start: 0.9106 (m) cc_final: 0.8846 (p) REVERT: C 634 ARG cc_start: 0.7657 (tpp80) cc_final: 0.7247 (mmt90) REVERT: C 796 ASP cc_start: 0.8106 (t0) cc_final: 0.7749 (t0) REVERT: C 814 LYS cc_start: 0.8571 (mptt) cc_final: 0.8323 (mmpt) REVERT: C 912 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8486 (p) REVERT: C 933 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8555 (mttp) REVERT: C 950 ASP cc_start: 0.8544 (t0) cc_final: 0.7845 (t0) REVERT: C 954 GLN cc_start: 0.8658 (mt0) cc_final: 0.8237 (mt0) REVERT: C 988 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7766 (mm-30) REVERT: C 1148 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6676 (t80) outliers start: 106 outliers final: 54 residues processed: 516 average time/residue: 0.5405 time to fit residues: 331.6323 Evaluate side-chains 500 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 436 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 49 optimal weight: 0.8980 chunk 225 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 268 optimal weight: 0.9990 chunk 147 optimal weight: 0.0010 chunk 118 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 289 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 277 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN A 137 ASN A 196 ASN A 245 HIS A 317 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN C 188 ASN C 245 HIS C 317 ASN C 437 ASN C 460 ASN C 644 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.107103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.086112 restraints weight = 57749.260| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.13 r_work: 0.3183 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27747 Z= 0.157 Angle : 0.754 13.414 37912 Z= 0.364 Chirality : 0.046 0.342 4505 Planarity : 0.004 0.052 4728 Dihedral : 8.007 99.244 5475 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.71 % Favored : 95.13 % Rotamer: Outliers : 3.28 % Allowed : 19.63 % Favored : 77.09 % 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: -0.25 (0.14), residues: 3245 helix: 1.87 (0.20), residues: 743 sheet: -0.19 (0.18), residues: 688 loop : -1.04 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 214 TYR 0.028 0.001 TYR A 369 PHE 0.031 0.001 PHE B 456 TRP 0.032 0.001 TRP A 436 HIS 0.014 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00360 (27612) covalent geometry : angle 0.71858 (37550) SS BOND : bond 0.00456 ( 43) SS BOND : angle 2.51782 ( 86) hydrogen bonds : bond 0.03753 ( 1120) hydrogen bonds : angle 5.57262 ( 3144) link_ALPHA1-4 : bond 0.01569 ( 6) link_ALPHA1-4 : angle 4.28750 ( 18) link_BETA1-4 : bond 0.00266 ( 28) link_BETA1-4 : angle 1.36688 ( 84) link_BETA1-6 : bond 0.01866 ( 3) link_BETA1-6 : angle 2.16635 ( 9) link_NAG-ASN : bond 0.00320 ( 55) link_NAG-ASN : angle 2.56700 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 459 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8287 (mmm160) cc_final: 0.7996 (mmt-90) REVERT: A 115 GLN cc_start: 0.8238 (mp10) cc_final: 0.7888 (mp10) REVERT: A 298 GLU cc_start: 0.8373 (tt0) cc_final: 0.7963 (tm-30) REVERT: A 319 ARG cc_start: 0.8666 (ttm110) cc_final: 0.8419 (ttm110) REVERT: A 394 ASN cc_start: 0.8137 (p0) cc_final: 0.7727 (p0) REVERT: A 395 VAL cc_start: 0.8387 (t) cc_final: 0.7877 (t) REVERT: A 448 ASN cc_start: 0.6350 (m-40) cc_final: 0.5947 (m110) REVERT: A 586 ASP cc_start: 0.8218 (m-30) cc_final: 0.7830 (m-30) REVERT: A 790 LYS cc_start: 0.8746 (mmmm) cc_final: 0.8514 (mtmm) REVERT: A 808 ASP cc_start: 0.8300 (t0) cc_final: 0.7900 (t0) REVERT: A 918 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: A 988 GLU cc_start: 0.8326 (mp0) cc_final: 0.7697 (mp0) REVERT: A 994 ASP cc_start: 0.8560 (t70) cc_final: 0.8254 (t0) REVERT: A 995 ARG cc_start: 0.8709 (mtt-85) cc_final: 0.8395 (mtp180) REVERT: A 1144 GLU cc_start: 0.7721 (pp20) cc_final: 0.7493 (pp20) REVERT: A 1146 ASP cc_start: 0.8144 (m-30) cc_final: 0.7882 (m-30) REVERT: B 41 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8412 (mtmt) REVERT: B 137 ASN cc_start: 0.8841 (t0) cc_final: 0.8342 (t0) REVERT: B 190 ARG cc_start: 0.7899 (mtt90) cc_final: 0.7562 (tpp-160) REVERT: B 319 ARG cc_start: 0.8852 (ttm110) cc_final: 0.8645 (ttm-80) REVERT: B 408 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.8075 (ptm-80) REVERT: B 467 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7303 (p0) REVERT: B 586 ASP cc_start: 0.8393 (m-30) cc_final: 0.8134 (m-30) REVERT: B 646 ARG cc_start: 0.8806 (mtm-85) cc_final: 0.8471 (mtm110) REVERT: B 725 GLU cc_start: 0.8548 (tt0) cc_final: 0.8328 (tt0) REVERT: B 855 PHE cc_start: 0.6632 (OUTLIER) cc_final: 0.6385 (p90) REVERT: B 912 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8481 (p) REVERT: B 994 ASP cc_start: 0.8491 (t70) cc_final: 0.8205 (t0) REVERT: B 1072 GLU cc_start: 0.8708 (pm20) cc_final: 0.8271 (pm20) REVERT: B 1118 ASP cc_start: 0.8591 (t70) cc_final: 0.8379 (t0) REVERT: C 121 ASN cc_start: 0.7822 (t0) cc_final: 0.7565 (t0) REVERT: C 138 ASP cc_start: 0.8447 (m-30) cc_final: 0.8175 (m-30) REVERT: C 187 LYS cc_start: 0.8789 (mtmm) cc_final: 0.8469 (ttpt) REVERT: C 269 TYR cc_start: 0.8558 (m-10) cc_final: 0.8236 (m-80) REVERT: C 574 ASP cc_start: 0.8150 (p0) cc_final: 0.7651 (t0) REVERT: C 586 ASP cc_start: 0.8281 (m-30) cc_final: 0.8043 (m-30) REVERT: C 602 THR cc_start: 0.9103 (m) cc_final: 0.8849 (p) REVERT: C 634 ARG cc_start: 0.7651 (tpp80) cc_final: 0.7188 (mmt90) REVERT: C 796 ASP cc_start: 0.8115 (t0) cc_final: 0.7757 (t0) REVERT: C 804 GLN cc_start: 0.8372 (mm110) cc_final: 0.8139 (mm-40) REVERT: C 814 LYS cc_start: 0.8573 (mptt) cc_final: 0.8324 (mmpt) REVERT: C 912 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8491 (p) REVERT: C 933 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8556 (mttp) REVERT: C 950 ASP cc_start: 0.8552 (t0) cc_final: 0.7933 (t0) REVERT: C 954 GLN cc_start: 0.8655 (mt0) cc_final: 0.8261 (mt0) REVERT: C 988 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7772 (mm-30) REVERT: C 1148 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6677 (t80) outliers start: 94 outliers final: 53 residues processed: 514 average time/residue: 0.5480 time to fit residues: 333.5755 Evaluate side-chains 502 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 440 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 202 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 83 optimal weight: 0.0070 chunk 78 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 325 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 196 ASN A 317 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B1101 HIS C 115 GLN C 245 HIS C 437 ASN C 460 ASN C 644 GLN C 675 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.106518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.085362 restraints weight = 57938.287| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.17 r_work: 0.3170 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 27747 Z= 0.189 Angle : 0.777 14.646 37912 Z= 0.374 Chirality : 0.047 0.342 4505 Planarity : 0.004 0.058 4728 Dihedral : 7.902 99.609 5475 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.30 % Favored : 94.55 % Rotamer: Outliers : 3.03 % Allowed : 20.22 % Favored : 76.74 % 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: -0.30 (0.14), residues: 3245 helix: 1.77 (0.19), residues: 749 sheet: -0.21 (0.18), residues: 683 loop : -1.07 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 983 TYR 0.030 0.002 TYR C 453 PHE 0.019 0.001 PHE C 486 TRP 0.033 0.002 TRP A 436 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00437 (27612) covalent geometry : angle 0.74301 (37550) SS BOND : bond 0.00439 ( 43) SS BOND : angle 2.52791 ( 86) hydrogen bonds : bond 0.03848 ( 1120) hydrogen bonds : angle 5.59507 ( 3144) link_ALPHA1-4 : bond 0.01589 ( 6) link_ALPHA1-4 : angle 4.21893 ( 18) link_BETA1-4 : bond 0.00237 ( 28) link_BETA1-4 : angle 1.41761 ( 84) link_BETA1-6 : bond 0.01838 ( 3) link_BETA1-6 : angle 2.22299 ( 9) link_NAG-ASN : bond 0.00343 ( 55) link_NAG-ASN : angle 2.56729 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 449 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8379 (mmm160) cc_final: 0.8104 (mmt-90) REVERT: A 298 GLU cc_start: 0.8348 (tt0) cc_final: 0.7944 (tm-30) REVERT: A 319 ARG cc_start: 0.8689 (ttm110) cc_final: 0.8437 (ttm110) REVERT: A 394 ASN cc_start: 0.8153 (p0) cc_final: 0.7724 (p0) REVERT: A 442 ASP cc_start: 0.5675 (t70) cc_final: 0.5167 (t0) REVERT: A 448 ASN cc_start: 0.6424 (m-40) cc_final: 0.5908 (m110) REVERT: A 586 ASP cc_start: 0.8236 (m-30) cc_final: 0.7809 (m-30) REVERT: A 790 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8493 (mtmm) REVERT: A 808 ASP cc_start: 0.8282 (t0) cc_final: 0.7878 (t0) REVERT: A 918 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: A 988 GLU cc_start: 0.8314 (mp0) cc_final: 0.7666 (mp0) REVERT: A 994 ASP cc_start: 0.8580 (t70) cc_final: 0.8273 (t0) REVERT: A 995 ARG cc_start: 0.8722 (mtt-85) cc_final: 0.8401 (mtp180) REVERT: A 1041 ASP cc_start: 0.8493 (m-30) cc_final: 0.8282 (m-30) REVERT: A 1045 LYS cc_start: 0.8937 (tppp) cc_final: 0.8666 (tppp) REVERT: B 41 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8415 (mtmt) REVERT: B 137 ASN cc_start: 0.8827 (t0) cc_final: 0.7979 (t0) REVERT: B 205 SER cc_start: 0.9047 (p) cc_final: 0.8841 (t) REVERT: B 319 ARG cc_start: 0.8849 (ttm110) cc_final: 0.8640 (ttm-80) REVERT: B 408 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7990 (ptm-80) REVERT: B 467 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7322 (p0) REVERT: B 586 ASP cc_start: 0.8378 (m-30) cc_final: 0.8117 (m-30) REVERT: B 646 ARG cc_start: 0.8837 (mtm-85) cc_final: 0.8494 (mtm110) REVERT: B 675 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7219 (mt0) REVERT: B 725 GLU cc_start: 0.8559 (tt0) cc_final: 0.8334 (tt0) REVERT: B 855 PHE cc_start: 0.6675 (OUTLIER) cc_final: 0.6425 (p90) REVERT: B 912 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8463 (p) REVERT: B 994 ASP cc_start: 0.8478 (t70) cc_final: 0.8182 (t0) REVERT: B 1072 GLU cc_start: 0.8748 (pm20) cc_final: 0.8287 (pm20) REVERT: B 1118 ASP cc_start: 0.8605 (t70) cc_final: 0.8398 (t0) REVERT: C 121 ASN cc_start: 0.7861 (t0) cc_final: 0.7599 (t0) REVERT: C 138 ASP cc_start: 0.8468 (m-30) cc_final: 0.8183 (m-30) REVERT: C 187 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8477 (ttpt) REVERT: C 269 TYR cc_start: 0.8579 (m-10) cc_final: 0.8319 (m-80) REVERT: C 574 ASP cc_start: 0.8165 (p0) cc_final: 0.7666 (t0) REVERT: C 586 ASP cc_start: 0.8287 (m-30) cc_final: 0.8033 (m-30) REVERT: C 602 THR cc_start: 0.9122 (m) cc_final: 0.8861 (p) REVERT: C 634 ARG cc_start: 0.7675 (tpp80) cc_final: 0.7260 (mmt90) REVERT: C 796 ASP cc_start: 0.8131 (t0) cc_final: 0.7773 (t0) REVERT: C 814 LYS cc_start: 0.8576 (mptt) cc_final: 0.8307 (mmpt) REVERT: C 933 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8533 (mttp) REVERT: C 950 ASP cc_start: 0.8551 (t0) cc_final: 0.7901 (t0) REVERT: C 954 GLN cc_start: 0.8650 (mt0) cc_final: 0.8232 (mt0) REVERT: C 1148 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6718 (t80) outliers start: 87 outliers final: 55 residues processed: 493 average time/residue: 0.6081 time to fit residues: 352.5063 Evaluate side-chains 507 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 444 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 293 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 236 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 211 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 297 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 957 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 394 ASN B 417 ASN B 519 HIS C 245 HIS C 437 ASN C 439 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 675 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.106731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.085748 restraints weight = 57577.973| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.14 r_work: 0.3179 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27747 Z= 0.178 Angle : 0.785 17.220 37912 Z= 0.379 Chirality : 0.047 0.308 4505 Planarity : 0.004 0.057 4728 Dihedral : 7.799 99.821 5475 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.84 % Favored : 95.01 % Rotamer: Outliers : 2.86 % Allowed : 20.71 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.31 (0.14), residues: 3245 helix: 1.80 (0.19), residues: 749 sheet: -0.23 (0.18), residues: 679 loop : -1.08 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 214 TYR 0.033 0.002 TYR A 369 PHE 0.038 0.001 PHE A 135 TRP 0.032 0.002 TRP A 436 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00413 (27612) covalent geometry : angle 0.75194 (37550) SS BOND : bond 0.00467 ( 43) SS BOND : angle 2.57150 ( 86) hydrogen bonds : bond 0.03827 ( 1120) hydrogen bonds : angle 5.61035 ( 3144) link_ALPHA1-4 : bond 0.01614 ( 6) link_ALPHA1-4 : angle 4.16589 ( 18) link_BETA1-4 : bond 0.00274 ( 28) link_BETA1-4 : angle 1.37787 ( 84) link_BETA1-6 : bond 0.01797 ( 3) link_BETA1-6 : angle 2.18125 ( 9) link_NAG-ASN : bond 0.00324 ( 55) link_NAG-ASN : angle 2.53991 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 448 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8498 (mmm160) cc_final: 0.8058 (mmt-90) REVERT: A 191 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7226 (mp0) REVERT: A 289 VAL cc_start: 0.9218 (OUTLIER) cc_final: 0.8948 (m) REVERT: A 298 GLU cc_start: 0.8389 (tt0) cc_final: 0.7956 (tm-30) REVERT: A 319 ARG cc_start: 0.8690 (ttm110) cc_final: 0.8377 (ttm110) REVERT: A 394 ASN cc_start: 0.8154 (p0) cc_final: 0.7725 (p0) REVERT: A 448 ASN cc_start: 0.6413 (m-40) cc_final: 0.6139 (m110) REVERT: A 586 ASP cc_start: 0.8223 (m-30) cc_final: 0.7781 (m-30) REVERT: A 790 LYS cc_start: 0.8682 (mmmm) cc_final: 0.8364 (mtpp) REVERT: A 808 ASP cc_start: 0.8243 (t0) cc_final: 0.7802 (t0) REVERT: A 814 LYS cc_start: 0.8911 (mmpt) cc_final: 0.8674 (mmpt) REVERT: A 918 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: A 950 ASP cc_start: 0.8474 (m-30) cc_final: 0.8145 (m-30) REVERT: A 988 GLU cc_start: 0.8286 (mp0) cc_final: 0.7632 (mp0) REVERT: A 994 ASP cc_start: 0.8568 (t70) cc_final: 0.8253 (t0) REVERT: A 995 ARG cc_start: 0.8726 (mtt-85) cc_final: 0.8404 (mtp180) REVERT: A 1045 LYS cc_start: 0.8895 (tppp) cc_final: 0.8683 (tppp) REVERT: A 1146 ASP cc_start: 0.8134 (m-30) cc_final: 0.7881 (m-30) REVERT: B 41 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8429 (mtmt) REVERT: B 137 ASN cc_start: 0.8780 (t0) cc_final: 0.7930 (t0) REVERT: B 190 ARG cc_start: 0.8460 (mpt180) cc_final: 0.8248 (tpt170) REVERT: B 319 ARG cc_start: 0.8893 (ttm110) cc_final: 0.8685 (ttm-80) REVERT: B 408 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8011 (ptm-80) REVERT: B 467 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7271 (p0) REVERT: B 586 ASP cc_start: 0.8356 (m-30) cc_final: 0.8092 (m-30) REVERT: B 646 ARG cc_start: 0.8817 (mtm-85) cc_final: 0.8455 (mtp85) REVERT: B 661 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7739 (tm-30) REVERT: B 675 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7193 (mt0) REVERT: B 725 GLU cc_start: 0.8552 (tt0) cc_final: 0.8322 (tt0) REVERT: B 855 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.6495 (p90) REVERT: B 912 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8434 (p) REVERT: B 994 ASP cc_start: 0.8460 (t70) cc_final: 0.8171 (t0) REVERT: B 1072 GLU cc_start: 0.8751 (pm20) cc_final: 0.8277 (pm20) REVERT: B 1118 ASP cc_start: 0.8568 (t70) cc_final: 0.8359 (t0) REVERT: C 121 ASN cc_start: 0.7906 (t0) cc_final: 0.7628 (t0) REVERT: C 138 ASP cc_start: 0.8440 (m-30) cc_final: 0.8149 (m-30) REVERT: C 187 LYS cc_start: 0.8806 (mtmm) cc_final: 0.8488 (ttpt) REVERT: C 231 ILE cc_start: 0.9434 (pp) cc_final: 0.9143 (mp) REVERT: C 269 TYR cc_start: 0.8584 (m-10) cc_final: 0.8323 (m-80) REVERT: C 574 ASP cc_start: 0.8168 (p0) cc_final: 0.7650 (t0) REVERT: C 586 ASP cc_start: 0.8280 (m-30) cc_final: 0.8028 (m-30) REVERT: C 602 THR cc_start: 0.9119 (m) cc_final: 0.8863 (p) REVERT: C 634 ARG cc_start: 0.7665 (tpp80) cc_final: 0.7244 (mmt90) REVERT: C 702 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7894 (tm-30) REVERT: C 796 ASP cc_start: 0.8139 (t0) cc_final: 0.7769 (t0) REVERT: C 814 LYS cc_start: 0.8568 (mptt) cc_final: 0.8241 (mmpt) REVERT: C 912 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8457 (p) REVERT: C 933 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8511 (mttp) REVERT: C 950 ASP cc_start: 0.8513 (t0) cc_final: 0.7862 (t0) REVERT: C 954 GLN cc_start: 0.8654 (mt0) cc_final: 0.8233 (mt0) REVERT: C 988 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7826 (mm-30) REVERT: C 1148 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.6648 (t80) outliers start: 82 outliers final: 53 residues processed: 495 average time/residue: 0.5932 time to fit residues: 345.5674 Evaluate side-chains 502 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 439 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 122 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 219 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 223 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 269 optimal weight: 0.0040 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 957 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 394 ASN B 519 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 437 ASN C 460 ASN C 644 GLN C 675 GLN C 957 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.107709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.086733 restraints weight = 57024.676| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.12 r_work: 0.3196 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27747 Z= 0.151 Angle : 0.784 16.354 37912 Z= 0.377 Chirality : 0.046 0.307 4505 Planarity : 0.004 0.054 4728 Dihedral : 7.515 99.307 5475 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.87 % Favored : 94.98 % Rotamer: Outliers : 2.51 % Allowed : 21.48 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3245 helix: 1.87 (0.20), residues: 750 sheet: -0.15 (0.19), residues: 681 loop : -1.07 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 214 TYR 0.031 0.001 TYR C 453 PHE 0.039 0.001 PHE A 135 TRP 0.041 0.002 TRP A 436 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00347 (27612) covalent geometry : angle 0.75115 (37550) SS BOND : bond 0.00413 ( 43) SS BOND : angle 2.76201 ( 86) hydrogen bonds : bond 0.03704 ( 1120) hydrogen bonds : angle 5.57231 ( 3144) link_ALPHA1-4 : bond 0.01587 ( 6) link_ALPHA1-4 : angle 4.06976 ( 18) link_BETA1-4 : bond 0.00284 ( 28) link_BETA1-4 : angle 1.30851 ( 84) link_BETA1-6 : bond 0.01836 ( 3) link_BETA1-6 : angle 2.14408 ( 9) link_NAG-ASN : bond 0.00302 ( 55) link_NAG-ASN : angle 2.45235 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9689.32 seconds wall clock time: 165 minutes 46.61 seconds (9946.61 seconds total)